No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.

EcoSal Plus

Domain 3:


Nucleotides, Nucleosides, and Nucleobases

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • Authors: Kaj Frank Jensen1, Gert Dandanell2, Bjarne Hove-Jensen3, and Martin WillemoËs4
  • Editor: Valley Stewart5
    Affiliations: 1: Department of Biology, University of Copenhagen, Copenhagen, Denmark; 2: Department of Biology, University of Copenhagen, Copenhagen, Denmark; 3: Department of Biology, University of Copenhagen, Copenhagen, Denmark; 4: Department of Biology, University of Copenhagen, Copenhagen, Denmark; 5: University of California, Davis, Davis, CA
  • Received 07 February 2008 Accepted 27 May 2008 Published 18 August 2008
  • Address correspondence to Kaj Frank Jensen [email protected]
image of Nucleotides, Nucleosides, and Nucleobases
    Preview this reference work article:
    Zoom in

    Nucleotides, Nucleosides, and Nucleobases, Page 1 of 2

    | /docserver/preview/fulltext/ecosalplus/3/1/3_6_2_module-1.gif /docserver/preview/fulltext/ecosalplus/3/1/3_6_2_module-2.gif
  • Abstract:

    We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in and ,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the -glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.

  • Citation: Jensen K, Dandanell G, Hove-Jensen B, WillemoËs M. 2008. Nucleotides, Nucleosides, and Nucleobases, EcoSal Plus 2008; doi:10.1128/ecosalplus.3.6.2


1. Jensen KF. 1983. Metabolism of 5-phosphoribosyl 1-pyrophosphate (PRPP) in Escherichia coli and Salmonella typhimurium, p 1–25. In Munch-Petersen A (ed), Metabolism of Nucleotides, Nucleosides and Nucleobases in Microorganisms. Academic Press, London, United Kingdom.
2. Bochner BR, Ames BN. 1982. Complete analysis of cellular nucleotides by two-dimensional thin layer chromatography. J Biol Chem 257:9759–9769.[PubMed]
3. Neuhard J, Nygaard P. 1987. Purines and pyrimidines, p 445–473. In Neidhardt FC, Ingraham JL, Low KB, Magasanik B, Schaechter M, and Umbarger HE (ed), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, vol. 1. American Society of Microbiology, Washington, DC.
4. Ingraham JL, Maaløe O, Neidhardt FC. 1983. Growth of the Bacterial Cell. Sinauer Associates, Inc., Sunderland, MA.
5. Neuhard J, Kelln RA. 1996. Biosynthesis and conversion of pyrimidines, p 580–599. In Curtis R III, Ingraham JL, Lin ECC, Brooks Low K, Magasanik B, Reznikoff WS, Riley M, Schaechter M, and Umbarger HE (ed), Escherichia coli and Salmonella: Cellular and Molecular Biology, vol. 1. ASM Press, Washington, DC.
6. Zalkin H, Nygaard P. 1996. Biosynthesis of purine nucleotides, p 561–579. In Curtis R III, Ingraham JL, Lin ECC, Brooks Low K, Magasanik B, Reznikoff WS, Riley M, Schaechter M, and Umbarger HE (ed), Escherichia coli and Salmonella: Cellular and Molecular Biology, vol. 1. ASM Press, Washington, DC.
7. Lieberman I, Kornberg A, Simms ES. 1955. Enzymatic synthesis of pyrimidine nucleotides; orotidine-5′-phosphate and uridine-5′-phosphate. J Biol Chem 215:403–451.[PubMed]
8. Hove-Jensen B. 1983. Chromosomal location of the gene encoding phosphoribosylpyrophosphate synthetase in Escherichia coli. J Bacteriol 154:177–184.[PubMed]
9. Hove-Jensen B, Nygaard P. 1982. Phosphoribosylpyrophosphate synthetase of Escherichia coli, Identification of a mutant enzyme. Eur J Biochem 126:327–332.[PubMed]
10. Jochimsen BU, Hove-Jensen B, Garber BB, Gots JS. 1985. Characterization of a Salmonella typhimurium mutant defective in phosphoribosylpyrophosphate synthetase. J Gen Microbiol 131:245–252.[PubMed]
11. Hove-Jensen B. 1988. Mutation in the phosphoribosylpyrophosphate synthetase gene ( prs) that results in simultaneous requirements for purine and pyrimidine nucleosides, nicotinamide nucleotide, histidine, and tryptophan in Escherichia coli. J Bacteriol 170:1148–1152.[PubMed]
12. Bower SG, Harlow KW, Switzer RL, Hove-Jensen B. 1989. Characterization of the Escherichia coli prsA1-encoded mutant phosphoribosylpyrophosphate synthetase identifies a divalent cation-nucleotide binding site. J Biol Chem 264:10287–10291.[PubMed]
13. Hove-Jensen B, Nygaard P. 1989. Role of guanosine kinase in the utilization of guanosine for nucleotide synthesis in Escherichia coli. J Gen Microbiol 135:1263–1273.[PubMed]
14. Post DA, Switzer RL, Hove-Jensen B. 1996. The defective phosphoribosyl diphosphate synthase in a temperature-sensitive prs-2 mutant of Escherichia coli is compensated by increased enzyme synthesis. Microbiology 142(Pt 2) :359–365. [CrossRef]
15. Post DA, Switzer RL. 1991. prsB is an allele of the Salmonella typhimurium prsA gene: characterization of a mutant phosphoribosylpyrophosphate synthetase. J Bacteriol 173:1978–1986.[PubMed]
16. White MN, Olszowy J, Switzer RL. 1971. Regulation and mechanism of phosphoribosylpyrophosphate synthetase: repression by end products. J Bacteriol 108:122–131.[PubMed]
17. Olszowy J, Switzer RL. 1972. Specific repression of phosphoribosylpyrophosphate synthetase by uridine compounds in Salmonella typhimurium. J Bacteriol 110:450–451.[PubMed]
18. He B, Choi KY, Zalkin H. 1993. Regulation of Escherichia coli glnB, prsA, and speA by the purine repressor. J Bacteriol 175:3598–3606.[PubMed]
19. Krath BN, Hove-Jensen B. 2001. Class II recombinant phosphoribosyl diphosphate synthase from spinach. Phosphate independence and diphosphoryl donor specificity. J Biol Chem 276:17851–17856. [PubMed][CrossRef]
20. Krath BN, Hove-Jensen B. 2001. Implications of secondary structure prediction and amino acid sequence comparison of class I and class II phosphoribosyl diphosphate synthases on catalysis, regulation, and quaternary structure. Protein Sci 10:2317–2324. [PubMed][CrossRef]
21. Gibson KJ, Schubert KR, Switzer RL. 1982. Binding of the substrates and the allosteric inhibitor adenosine 5′-diphosphate to phosphoribosylpyrophosphate synthetase from Salmonella typhimurium. J Biol Chem 257:2391–2396.[PubMed]
22. Hove-Jensen B, Harlow KW, King CJ, Switzer RL. 1986. Phosphoribosylpyrophosphate synthetase of Escherichia coli. Properties of the purified enzyme and primary structure of the prs gene. J Biol Chem 261:6765–6771.[PubMed]
23. Switzer RL. 1971. Regulation and mechanism of phosphoribosylpyrophosphate synthetase. 3 Kinetic studies of the reaction mechanism. J Biol Chem 246:2447–2458.[PubMed]
24. Switzer RL. 1969. Regulation and mechanism of phosphoribosylpyrophosphate synthetase. I. Purification and properties of the enzyme from Salmonella typhimurium. J Biol Chem 244:2854–2863.[PubMed]
25. Switzer RL, Sogin DC. 1973. Regulation and mechanism of phosphoribosylpyrophosphate synthetase. V. Inhibition by end products and regulation by adenosine diphosphate. J Biol Chem 248:1063–1073.[PubMed]
26. Willemoës M, Hove-Jensen B. 1997. Binding of divalent magnesium by Escherichia coli phosphoribosyl diphosphate synthetase. Biochemistry 36:5078–5083. [PubMed][CrossRef]
27. Willemoës M, Hove-Jensen B, Larsen S. 2000. Steady state kinetic model for the binding of substrates and allosteric effectors to Escherichia coli phosphoribosyl-diphosphate synthase. J Biol Chem 275:35408–35412. [PubMed][CrossRef]
28. Eriksen TA, Kadziola A, Bentsen AK, Harlow KW, Larsen S. 2000. Structural basis for the function of Bacillus subtilis phosphoribosyl-pyrophosphate synthetase. Nat Struct Biol 7:303–308. [PubMed][CrossRef]
29. Smith JL. 1999. Forming and inhibiting PRT active sites. Nat Struct Biol 6:502–504. [PubMed][CrossRef]
30. Eriksen TA, Kadziola A, Larsen S. 2002. Binding of cations in Bacillus subtilis phosphoribosyldiphosphate synthetase and their role in catalysis. Protein Sci 11:271–279. [PubMed][CrossRef]
31. Willemoës M, Nilsson D, Hove-Jensen B. 1996. Effects of mutagenesis of aspartic acid residues in the putative phosphoribosyl diphosphate binding site of Escherichia coli phosphoribosyl diphosphate synthetase on metal ion specificity and ribose 5-phosphate binding. Biochemistry 35:8181–8186. [PubMed][CrossRef]
32. Hove-Jensen B, Bentsen AK, Harlow KW. 2005. Catalytic residues Lys197 and Arg199 of Bacillus subtilis phosphoribosyl diphosphate synthase. Alanine-scanning mutagenesis of the flexible catalytic loop. FEBS J 272:3631–3639. [PubMed][CrossRef]
33. Hilden I, Hove-Jensen B, Harlow KW. 1995. Inactivation of Escherichia coli phosphoribosylpyrophosphate synthetase by the 2′,3′-dialdehyde derivative of ATP. Identification of active site lysines. J Biol Chem 270:20730–20736. [PubMed][CrossRef]
34. Nygaard FB. 2001. The molecular mechanism of catalysis and allosteric regulation in the phosphoribosyl-diphosphate synthase from Bacillus subtilis. University of Copenhagen, Copenhagen, Denmark.
35. Hove-Jensen B, Rosenkrantz TJ, Haldimann A, Wanner BL. 2003. Escherichia coli phnN, encoding ribose 1,5-bisphosphokinase activity (phosphoribosyl diphosphate forming): dual role in phosphonate degradation and NAD biosynthesis pathways. J Bacteriol 185:2793–2801. [PubMed][CrossRef]
36. Hove-Jensen B. 1989. Phosphoribosylpyrophosphate (PRPP)-less mutants of Escherichia coli. Mol Microbiol 3:1487–1492. [PubMed][CrossRef]
37. Bower SG, Hove-Jensen B, Switzer RL. 1988. Structure of the gene encoding phosphoribosylpyrophosphate synthetase ( prsA) in Salmonella typhimurium. J Bacteriol 170:3243–3248.[PubMed]
38. Switzer RL, Gibson KJ. 1978. Phosphoribosylpyrophosphate synthetase (ribose-5-phosphate pyrophosphokinase) from Salmonella typhimurium. Methods Enzymol 51:3–11. [PubMed][CrossRef]
39. Krahn JM, Kim JH, Burns MR, Parry RJ, Zalkin H, Smith JL. 1997. Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site. Biochemistry 36:11061–11068. [PubMed][CrossRef]
40. Messenger LJ, Zalkin H. 1979. Glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Purification and properties. J Biol Chem 254:3382–3392.[PubMed]
41. Muchmore CR, Krahn JM, Kim JH, Zalkin H, Smith JL. 1998. Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Protein Sci 7:39–51.[PubMed]
42. Zalkin H, Smith JL. 1998. Enzymes utilizing glutamine as an amide donor. Adv Enzymol Relat Areas Mol Biol 72:87–144. [PubMed][CrossRef]
43. Zhou G, Smith JL, Zalkin H. 1994. Binding of purine nucleotides to two regulatory sites results in synergistic feedback inhibition of glutamine 5-phosphoribosylpyrophosphate amidotransferase. J Biol Chem 269:6784–6789.[PubMed]
44. Henriksen A, Aghajari N, Jensen KF, Gajhede M. 1996. A flexible loop at the dimer interface is a part of the active site of the adjacent monomer of Escherichia coli orotate phosphoribosyltransferase. Biochemistry 35:3803–3809. [PubMed][CrossRef]
45. Poulsen P, Bonekamp F, Jensen KF. 1984. Structure of the Escherichia coli pyrE operon and control of pyrE expression by a UTP modulated intercistronic attentuation. EMBO J 3:1783–1790.[PubMed]
46. Poulsen P, Jensen KF, Valentin-Hansen P, Carlsson P, Lundberg LG. 1983. Nucleotide sequence of the Escherichia coli pyrE gene and of the DNA in front of the protein-coding region. Eur J Biochem 135:223–229. [PubMed][CrossRef]
47. Scapin G, Grubmeyer C, Sacchettini JC. 1994. Crystal structure of orotate phosphoribosyltransferase. Biochemistry 33:1287–1294. [PubMed][CrossRef]
48. Scapin G, Ozturk DH, Grubmeyer C, Sacchettini JC. 1995. The crystal structure of the orotate phosphoribosyltransferase complexed with orotate and alpha- D-5-phosphoribosyl-1-pyrophosphate. Biochemistry 34:10744–10754. [PubMed][CrossRef]
49. Vos S, de Jersey J, Martin JL. 1997. Crystal structure of Escherichia coli xanthine phosphoribosyltransferase. Biochemistry 36:4125–4134. [PubMed][CrossRef]
50. Vos S, Parry RJ, Burns MR, de Jersey J, Martin JL. 1998. Structures of free and complexed forms of Escherichia coli xanthine-guanine phosphoribosyltransferase. J Mol Biol 282:875–889. [PubMed][CrossRef]
51. Gots JS, Benson CE, Shumas SR. 1972. Genetic separation of hypoxanthine and guanine-xanthine phosphoribosyltransferase activities by deletion mutations in Salmonella typhimurium. J Bacteriol 112:910–916.[PubMed]
52. Guddat LW, Vos S, Martin JL, Keough DT, de Jersey J. 2002. Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. Protein Sci 11:1626–1638. [PubMed][CrossRef]
53. Jochimsen B, Nygaard P, Vestergaard T. 1975. Location on the chromosome of Escherichia coli of genes governing purine metabolism. Adenosine deaminase ( add), guanosine kinase ( gsk) and hypoxanthine phosphoribosyltransferase ( hpt). Mol Gen Genet 143:85–91. [PubMed][CrossRef]
54. Lee CC, Craig SP, III, Eakin AE. 1998. A single amino acid substitution in the human and a bacterial hypoxanthine phosphoribosyltransferase modulates specificity for the binding of guanine. Biochemistry 37:3491–3498. [PubMed][CrossRef]
55. Hershey HV, Taylor MW. 1986. Nucleotide sequence and deduced amino acid sequence of Escherichia coli adenine phosphoribosyltransferase and comparison with other analogous enzymes. Gene 43:287–293. [PubMed][CrossRef]
56. Shi W, Sarver AE, Wang CC, Tanaka KS, Almo SC, Schramm VL. 2002. Closed site complexes of adenine phosphoribosyltransferase from Giardia lamblia reveal a mechanism of ribosyl migration. J Biol Chem 277:39981–39988. [PubMed][CrossRef]
57. Jensen KF, Mygind B. 1996. Different oligomeric states are involved in the allosteric behavior of uracil phosphoribosyltransferase from Escherichia coli. Eur J Biochem 240:637–645. [PubMed][CrossRef]
58. Lundegaard C, Jensen KF. 1999. Kinetic mechanism of uracil phosphoribosyltransferase from Escherichia coli and catalytic importance of the conserved proline in the PRPP binding site. Biochemistry 38:3327–3334. [PubMed][CrossRef]
59. Schumacher MA, Bashor CJ, Song MH, Otsu K, Zhu S, Parry RJ, Ullman B, Brennan RG. 2002. The structural mechanism of GTP stabilized oligomerization and catalytic activation of the Toxoplasma gondii uracil phosphoribosyltransferase. Proc Natl Acad Sci USA 99:78–83. [PubMed][CrossRef]
60. Beck BJ, Huelsmeyer M, Paul S, Downs DM. 2003. A mutation in the essential gene gmk (encoding guanlyate kinase) generates a requirement for adenine at low temperature in Salmonella enterica. J Bacteriol 185:6732–6735. [PubMed][CrossRef]
61. Gentry D, Bengra C, Ikehara K, Cashel M. 1993. Guanylate kinase of Escherichia coli K-12. J Biol Chem 268:14316–14321.[PubMed]
62. Hible G, Daalova P, Gilles AM, Cherfils J. 2006. Crystal structures of GMP kinase in complex with ganciclovir monophosphate and Ap5G. Biochimie 88:1157–1164. [PubMed][CrossRef]
63. Hible G, Renault L, Schaeffer F, Christova P, Zoe Radulescu A, Evrin C, Gilles AM, Cherfils J. 2005. Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase. J Mol Biol 352:1044–1059. [PubMed][CrossRef]
64. Berry MB, Bae E, Bilderback TR, Glaser M, Phillips GN, Jr. 2006. Crystal structure of ADP/AMP complex of Escherichia coli adenylate kinase. Proteins 62:555–556. [PubMed][CrossRef]
65. Berry MB, Meador B, Bilderback T, Liang P, Glaser M, Phillips GN, Jr. 1994. The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP. Proteins 19:183–198. [PubMed][CrossRef]
66. Muller CW, Schulz GE. 1992. Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution. A model for a catalytic transition state. J Mol Biol 224:159–177. [PubMed][CrossRef]
67. Muller CW, Schulz GE. 1988. Structure of the complex of adenylate kinase from Escherichia coli with the inhibitor P1,P5-di(adenosine-5′-)pentaphosphate. J Mol Biol 202:909–912. [PubMed][CrossRef]
68. Saint Girons I, Gilles AM, Margarita D, Michelson S, Monnot M, Fermandjian S, Danchin A, Bârzu O. 1987. Structural and catalytic characteristics of Escherichia coli adenylate kinase. J Biol Chem 262:622–629.[PubMed]
69. Briozzo P, Evrin C, Meyer P, Assairi L, Joly N, Barzu O, Gilles AM. 2005. Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation. J Biol Chem 280:25533–25540. [PubMed][CrossRef]
70. Sakamoto H, Landais S, Evrin C, Laurent-Winter C, Bârzu O, Kelln RA. 2004. Structure-function relationships of UMP kinases from pyrH mutants of Gram-negative bacteria. Microbiology 150:2153–2159. [PubMed][CrossRef]
71. Serina L, Blondin C, Krin E, Sismeiro O, Danchin A, Sakamoto H, Gilles AM, Bârzu O. 1995. Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. Biochemistry 34:5066–5074. [PubMed][CrossRef]
72. Briozzo P, Golinelli-Pimpaneau B, Gilles AM, Gaucher JF, Burlacu-Miron S, Sakamoto H, Janin J, Barzu O. 1998. Structures of Escherichia coli CMP kinase alone and in complex with CDP: a new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity. Structure 6:1517–1527. [PubMed][CrossRef]
73. Fricke J, Neuhard J, Kelln RA, Pedersen S. 1995. The cmk gene encoding cytidine monophosphate kinase is located in the rpsA operon and is required for normal replication rate in Escherichia coli. J Bacteriol 177:517–523.[PubMed]
74. Lavie A, Ostermann N, Brundiers R, Goody RS, Reinstein J, Konrad M, Schlichting I. 1998. Structural basis for efficient phosphorylation of 3′-azidothymidine monophosphate by Escherichia coli thymidylate kinase. Proc Natl Acad Sci USA 95:14045–14050. [PubMed][CrossRef]
75. Reynes JP, Tiraby M, Baron M, Drocourt D, Tiraby G. 1996. Escherichia coli thymidylate kinase: molecular cloning, nucleotide sequence, and genetic organization of the corresponding tmk locus. J Bacteriol 178:2804–2812.[PubMed]
76. Almaula N, Lu Q, Delgado J, Belkin S, Inouye M. 1995. Nucleoside diphosphate kinase from Escherichia coli. J Bacteriol 177:2524–2529.[PubMed]
77. Moynie L, Giraud MF, Georgescauld F, Lascu I, Dautant A. 2007. The structure of the Escherichia coli nucleoside diphosphate kinase reveals a new quaternary architecture for this enzyme family. Proteins 67:755–765. [PubMed][CrossRef]
78. Blattner FR, Plunkett G III, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453–1474. [PubMed][CrossRef]
79. McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, Hou S, Layman D, Leonard S, Nguyen C, Scott K, Holmes A, Grewal N, Mulvaney E, Ryan E, Sun H, Florea L, Miller W, Stoneking T, Nhan M, Waterston R, Wilson RK. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413:852–856. [PubMed][CrossRef]
80. Grubmeyer C, Wang G. 1998. Making a nucleotide: structure and function of orotate phosphoribosyltransferase. Paths Pyrimidines 6(1) :1–11.
81. Schramm VL, Grubmeyer CT. 2004. Phosphoribosyltransferase mechanisms and roles in nucleic acid metabolism. Prog Nucleic Acids Res Mol Biol 77:261–304. [CrossRef]
82. Sinha SC, Smith JL. 2001. The PRT protein family. Curr Opin Struct Biol 11:733–739. [PubMed][CrossRef]
83. Heroux A, White EL, Ross LJ, Borhani DW. 1999. Crystal structures of the Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase-GMP and -IMP complexes: comparison of purine binding interactions with the XMP complex. Biochemistry 38:14485–14494. [PubMed][CrossRef]
84. Heroux A, White EL, Ross LJ, Davis RL, Borhani DW. 1999. Crystal structure of Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase with XMP, pyrophosphate, and two Mg 2+ ions bound: insights into the catalytic mechanism. Biochemistry 38:14495–14506. [PubMed][CrossRef]
85. Smith JL. 1998. Glutamine PRPP amidotransferase: snapshots of an enzyme in action. Curr Opin Struct Biol 8:686–694. [PubMed][CrossRef]
86. Hoffmeyer J, Neuhard J. 1971. Metabolism of exogenous purine bases and nucleosides by Salmonella typhimurium. J Bacteriol 106:14–24.[PubMed]
87. Jensen KF, Leer JC, Nygaard P. 1973. Thymine utilization in Escherichia coli K12 on the role of deoxyribose 1-phosphate and thymidine phosphorylase. Eur J Biochem 40:345–354. [PubMed][CrossRef]
88. Brune M, Schumann R, Wittinghofer F. 1985. Cloning and sequencing of the adenylate kinase gene ( adk) of Escherichia coli. Nucleic Acids Res 13:7139–7151. [PubMed][CrossRef]
89. Glaser M, Nulty W, Vagelos PR. 1975. Role of adenylate kinase in the regulation of macromolecular biosynthesis in a putative mutant of Escherichia coli defective in membrane phospholipid biosynthesis. J Bacteriol 123:128–136.[PubMed]
90. Ingraham JL, Neuhard J. 1972. Cold-sensitive mutants of Salmonella typhimurium defective in uridine monophosphate kinase ( pyrH). J Biol Chem 247:6259–6265.[PubMed]
91. Daws TD, Fuchs JA. 1984. Isolation and characterization of an Escherichia coli mutant deficient in dTMP kinase activity. J Bacteriol 157:440–444.[PubMed]
92. Beck CF, Neuhard J, Thomassen E, Ingraham JL, Kleker E. 1974. Salmonella typhimurium mutants defective in cytidine monophosphate kinase ( cmk). J Bacteriol 120:1370–1379.[PubMed]
93. Chapman AG, Fall L, Atkinson DE. 1971. Adenylate energy charge in Escherichia coli during growth and starvation. J Bacteriol 108:1072–1086.[PubMed]
94. Glembotski CC, Chapman AG, Atkinson DE. 1981. Adenylate energy charge in Escherichia coli CR341T28 and properties of heat-sensitive adenylate kinase. J Bacteriol 145:1374–1385.[PubMed]
95. Oeschger MP, Bessman MJ. 1966. Purification and properties of guanylate kinase from Escherichia coli. J Biol Chem 241:5452–5460.[PubMed]
96. Bucurenci N, Sakamoto H, Briozzo P, Palibroda N, Serina L, Sarfati RS, Labesse G, Briand G, Danchin A, Barzu O, Gilles AM. 1996. CMP kinase from Escherichia coli is structurally related to other nucleoside monophosphate kinases. J Biol Chem 271:2856–2862. [PubMed][CrossRef]
97. Nelson DJ, Carter CE. 1969. Purification and characterization of thymidine 5-monophosphate kinase from Escherichia coli B. J Biol Chem 244:5254–5262.[PubMed]
98. Fukami-Kobayashi K, Nosaka M, Nakazawa A, Go M. 1996. Ancient divergence of long and short isoforms of adenylate kinase: molecular evolution of the nucleoside monophosphate kinase family. FEBS Lett 385:214–220. [PubMed][CrossRef]
99. Traut TW. 1994. The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites. Eur J Biochem 222:9–19. [PubMed][CrossRef]
100. Byeon L, Shi Z, Tsai MD. 1995. Mechanism of adenylate kinase. The “essential lysine” helps to orient the phosphates and the active site residues to proper conformations. Biochemistry 34:3172–3182. [PubMed][CrossRef]
101. Evrin C, Straut M, Slavova-Azmanova N, Bucurenci N, Onu A, Assairi L, Ionescu M, Palibroda N, Barzu O, Gilles AM. 2007. Regulatory mechanisms differ in UMP kinases from gram-negative and gram-positive bacteria. J Biol Chem 282:7242–7253. [PubMed][CrossRef]
102. Hama H, Lerner C, Inouye S, Inouye M. 1991. Location of the gene ( ndk) for nucleoside diphosphate kinase on the physical map of the Escherichia coli chromosome. J Bacteriol 173:3276.
103. Rodriguez SB, Ingraham JL. 1983. Location on the Salmonella typhimurium chromosome of the gene encoding nucleoside diphosphokinase ( ndk). J Bacteriol 153:1101–1103.[PubMed]
104. Saeki T, Hori M, Umezawa H. 1974. Pyruvate kinase of Escherichia coli. Its role in supplying nucleoside triphosphates in cells under anaerobic conditions. J Biochem 76:631–637.[PubMed]
105. Kuroda A, Kornberg A. 1997. Polyphosphate kinase as a nucleoside diphosphate kinase in Escherichia coli and Pseudomonas aeruginosa. Proc Natl Acad Sci USA 94:439–442. [PubMed][CrossRef]
106. Bernard MA, Ray NB, Olcott MC, Hendricks SP, Mathews CK. 2000. Metabolic functions of microbial nucleoside diphosphate kinases. J Bioenerg Biomembr 32:259–267. [PubMed][CrossRef]
107. Lu Q, Inouye M. 1996. Adenylate kinase complements nucleoside diphosphate kinase deficiency in nucleotide metabolism. Proc Natl Acad Sci USA 93:5720–5725. [PubMed][CrossRef]
108. Willemoës M, Kilstrup M. 2005. Nucleoside triphosphate synthesis catalysed by adenylate kinase is ADP dependent. Arch Biochem Biophys 444:195–199. [PubMed][CrossRef]
109. Murakami K, Mitchell T, Nishimura JS. 1972. Nucleotide specificity of Escherichia coli succinic thiokinase. Succinyl coenzyme A-stimulated nucleoside diphosphate kinase activity of the enzyme. J Biol Chem 247:6247–6252.[PubMed]
110. Led JJ, Switon WK, Jensen KF. 1983. Phosphorolytic activity of Escherichia coli glycyl-tRNA synthetase towards its cognate aminoacyl adenylate detected by 31P-NMR spectroscopy and thin-layer chromatography. Eur J Biochem 136:469–479. [PubMed][CrossRef]
111. Hong ES, Yeung A, Funchain P, Slupska MM, Miller JH. 2005. Mutants with temperature-sensitive defects in the Escherichia coli mismatch repair system: sensitivity to mispairs generated in vivo. J Bacteriol 187:840–846. [PubMed][CrossRef]
112. Shen R, Wheeler LJ, Mathews CK. 2006. Molecular interactions involving Escherichia coli nucleoside diphosphate kinase. J Bioenerg Biomembr 38:255–259. [PubMed][CrossRef]
113. Zhang X, Lu Q, Inouye M, Mathews CK. 1996. Effects of T4 phage infection and anaerobiosis upon nucleotide pools and mutagenesis in nucleoside diphosphokinase-defective Escherichia coli strains. J Bacteriol 178:4115–4121.[PubMed]
114. Lu Q, Zhang X, Almaula N, Mathews CK, Inouye M. 1995. The gene for nucleoside diphosphate kinase functions as a mutator gene in Escherichia coli. J Mol Biol 254:337–341. [PubMed][CrossRef]
115. Lascu I, Gonin P. 2000. The catalytic mechanism of nucleoside diphosphate kinases. J Bioenerg Biomembr 32:237–246. [PubMed][CrossRef]
116. Xu YW, Morera S, Janin J, Cherfils J. 1997. AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP. Proc Natl Acad Sci USA 94:3579–3583. [PubMed][CrossRef]
117. Xu Y, Sellam O, Morera S, Sarfati S, Biondi R, Veron M, Janin J. 1997. X-ray analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase. Proc Natl Acad Sci USA 94:7162–7165. [PubMed][CrossRef]
118. Bennett SE, Chen CY, Mosbaugh DW. 2004. Escherichia coli nucleoside diphosphate kinase does not act as a uracil-processing DNA repair nuclease. Proc Natl Acad Sci USA 101:6391–6396. [PubMed][CrossRef]
119. Goswami SC, Yoon JH, Abramczyk BM, Pfeifer GP, Postel EH. 2006. Molecular and functional interactions between Escherichia coli nucleoside-diphosphate kinase and the uracil-DNA glycosylase Ung. J Biol Chem 281:32131–32139. [PubMed][CrossRef]
120. Kumar P, Krishna K, Srinivasan R, Ajitkumar P, Varshney U. 2004. Mycobacterium tuberculosis and Escherichia coli nucleoside diphosphate kinases lack multifunctional activities to process uracil containing DNA. DNA Repair (Amst.) 3:1483–1492. [PubMed][CrossRef]
121. Postel EH, Abramczyk BM. 2003. Escherichia coli nucleoside diphosphate kinase is a uracil-processing DNA repair nuclease. Proc Natl Acad Sci USA 100:13247–13252. [PubMed][CrossRef]
122. Buchanan JM, Ohnoki S, Hong BS. 1978. 2-Formamido-N-ribosylacetamide 5′-phosphate: L-glutamine amido-ligase (adenosine diphosphate). Methods Enzymol 51:193–201. [PubMed][CrossRef]
123. Fath MJ, Mahanty HK, Kolter R. 1989. Characterization of a purF operon mutation which affects colicin V production. J Bacteriol 171:3158–3161.[PubMed]
124. Makaroff CA, Zalkin H. 1985. Regulation of Escherichia coli purF. Analysis of the control region of a pur regulon gene. J Biol Chem 260:10378–10387.[PubMed]
125. Houlberg U, Hove-Jensen B, Jochimsen B, Nygaard P. 1983. Identification of the enzymatic reactions encoded by the purG and purI genes of Escherichia coli. J Bacteriol 154:1485–1488.[PubMed]
126. Cheng YS, Rudolph J, Stern M, Stubbe J, Flannigan KA, Smith JM. 1990. Glycinamide ribonucleotide synthetase from Escherichia coli: cloning, overproduction, sequencing, isolation, and characterization. Biochemistry 29:218–227. [PubMed][CrossRef]
127. Wang W, Kappock TJ, Stubbe J, Ealick SE. 1998. X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli. Biochemistry 37:15647–15662. [PubMed][CrossRef]
128. Almassy RJ, Janson CA, Kan CC, Hostomska Z. 1992. Structures of apo and complexed Escherichia coli glycinamide ribonucleotide transformylase. Proc Natl Acad Sci USA 89:6114–6118. [PubMed][CrossRef]
129. Inglese J, Johnson DL, Shiau A, Smith JM, Benkovic SJ. 1990. Subcloning, characterization, and affinity labeling of Escherichia coli glycinamide ribonucleotide transformylase. Biochemistry 29:1436–1443. [PubMed][CrossRef]
130. Smith JM, Daum HA, III. 1987. Identification and nucleotide sequence of a gene encoding 5′-phosphoribosylglycinamide transformylase in Escherichia coli K12. J Biol Chem 262:10565–10569.[PubMed]
131. Marolewski A, Smith JM, Benkovic SJ. 1994. Cloning and characterization of a new purine biosynthetic enzyme: a non-folate glycinamide ribonucleotide transformylase from E. coli Biochemistry 33:2531–2537. [PubMed][CrossRef]
132. Thoden JB, Firestine S, Nixon A, Benkovic SJ, Holden HM. 2000. Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase. Biochemistry 39:8791–8802. [PubMed][CrossRef]
133. Thoden JB, Firestine SM, Benkovic SJ, Holden HM. 2002. PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site. J Biol Chem 277:23898–23908. [PubMed][CrossRef]
134. Anand R, Hoskins AA, Stubbe J, Ealick SE. 2004. Domain organization of Salmonella typhimurium formylglycinamide ribonucleotide amidotransferase revealed by X-ray crystallography. Biochemistry 43:10328–10342. [PubMed][CrossRef]
135. Sampei G, Mizobuchi K. 1989. The organization of the purL gene encoding 5′-phosphoribosylformylglycinamide amidotransferase of Escherichia coli. J Biol Chem 264:21230–21238.[PubMed]
136. Schendel FJ, Mueller E, Stubbe J, Shiau A, Smith JM. 1989. Formylglycinamide ribonucleotide synthetase from Escherichia coli: cloning, sequencing, overproduction, isolation, and characterization. Biochemistry 28:2459–2471. [PubMed][CrossRef]
137. Li C, Kappock TJ, Stubbe J, Weaver TM, Ealick SE. 1999. X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 Å resolution. Structure 7:1155–1166. [PubMed][CrossRef]
138. Schrimsher JL, Schendel FJ, Stubbe J, Smith JM. 1986. Purification and characterization of aminoimidazole ribonucleotide synthetase from Escherichia coli. Biochemistry 25:4366–4371. [PubMed][CrossRef]
139. Meyer E, Kappock TJ, Osuji C, Stubbe J. 1999. Evidence for the direct transfer of the carboxylate of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to generate 4-carboxy-5-aminoimidazole ribonucleotide catalyzed by Escherichia coli PurE, an N5-CAIR mutase. Biochemistry 38:3012–3018. [PubMed][CrossRef]
140. Meyer E, Leonard NJ, Bhat B, Stubbe J, Smith JM. 1992. Purification and characterization of the purE, purK, and purC gene products: identification of a previously unrecognized energy requirement in the purine biosynthetic pathway. Biochemistry 31:5022–5032. [PubMed][CrossRef]
141. Thoden JB, Kappock TJ, Stubbe J, Holden HM. 1999. Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily. Biochemistry 38:15480–15492. [PubMed][CrossRef]
142. Hoskins AA, Morar M, Kappock TJ, Mathews II, Zaugg JB, Barder TE, Peng P, Okamoto A, Ealick SE, Stubbe J. 2007. N5-CAIR mutase: role of a CO 2 binding site and substrate movement in catalysis. Biochemistry 46:2842–2855. [PubMed][CrossRef]
143. Mathews II, Kappock TJ, Stubbe J, Ealick SE. 1999. Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway. Structure 7:1395–1406. [PubMed][CrossRef]
144. Ginder ND, Binkowski DJ, Fromm HJ, Honzatko RB. 2006. Nucleotide complexes of Escherichia coli phosphoribosylaminoimidazole succinocarboxamide synthetase. J Biol Chem 281:20680–20688. [PubMed][CrossRef]
145. Tiedeman AA, DeMarini DJ, Parker J, Smith JM. 1990. DNA sequence of the purC gene encoding 5′-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide synthetase and organization of the dapA-purC region of Escherichia coli K-12. J Bacteriol 172:6035–6041.[PubMed]
146. He B, Smith JM, Zalkin H. 1992. Escherichia coli purB gene: cloning, nucleotide sequence, and regulation by purR. J Bacteriol 174:130–136.[PubMed]
147. Tsai M, Koo J, Yip P, Colman RF, Segall ML, Howell PL. 2007. Substrate and product complexes of Escherichia coli adenylosuccinate lyase provide new insights into the enzymatic mechanism. J Mol Biol 370:541–554. [PubMed][CrossRef]
148. Aiba A, Mizobuchi K. 1989. Nucleotide sequence analysis of genes purH and purD involved in the de novo purine nucleotide biosynthesis of Escherichia coli. J Biol Chem 264:21239–21246.[PubMed]
149. Cheong CG, Wolan DW, Greasley SE, Horton PA, Beardsley GP, Wilson IA. 2004. Crystal structures of human bifunctional enzyme aminoimidazole-4-carboxamide ribonucleotide transformylase/IMP cyclohydrolase in complex with potent sulfonyl-containing antifolates. J Biol Chem 279:18034–18045. [PubMed][CrossRef]
150. Chopra AK, Peterson JW, Prasad R. 1991. Nucleotide sequence analysis of purH and purD genes from Salmonella typhimurium. Biochim Biophys Acta 1090:351–354.[PubMed]
151. Xu L, Chong Y, Hwang I, D’Onofrio A, Amore K, Beardsley GP, Li C, Olson AJ, Boger DL, Wilson IA. 2007. Structure-based design, synthesis, evaluation, and crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase. J Biol Chem 282:13033–13046. [PubMed][CrossRef]
152. Poland BW, Fromm HJ, Honzatko RB. 1996. Crystal structures of adenylosuccinate synthetase from Escherichia coli complexed with GDP, IMP hadacidin, NO 3 , and Mg 2+. J Mol Biol 264:1013–1027. [PubMed][CrossRef]
153. Poland BW, Hou Z, Bruns C, Fromm HJ, Honzatko RB. 1996. Refined crystal structures of guanine nucleotide complexes of adenylosuccinate synthetase from Escherichia coli. J Biol Chem 271:15407–15413. [PubMed][CrossRef]
154. Poland BW, Lee SF, Subramanian MV, Siehl DL, Anderson RJ, Fromm HJ, Honzatko RB. 1996. Refined crystal structure of adenylosuccinate synthetase from Escherichia coli complexed with hydantocidin 5′-phosphate, GDP, HPO 4( 2−), Mg 2+, and hadacidin. Biochemistry 35:15753–15759. [PubMed][CrossRef]
155. Wolfe SA, Smith JM. 1988. Nucleotide sequence and analysis of the purA gene encoding adenylosuccinate synthetase of Escherichia coli K12. J Biol Chem 263:19147–19153.[PubMed]
156. Gan L, Petsko GA, Hedstrom L. 2002. Crystal structure of a ternary complex of Tritrichomonas foetus inosine 5′-monophosphate dehydrogenase: NAD+ orients the active site loop for catalysis. Biochemistry 41:13309–13317. [PubMed][CrossRef]
157. Kerr KM, Cahoon M, Bosco DA, Hedstrom L. 2000. Monovalent cation activation in Escherichia coli inosine 5′-monophosphate dehydrogenase. Arch Biochem Biophys 375:131–137. [PubMed][CrossRef]
158. Sintchak MD, Fleming MA, Futer O, Raybuck SA, Chambers SP, Caron PR, Murcko MA, Wilson KP. 1996. Structure and mechanism of inosine monophosphate dehydrogenase in complex with the immunosuppressant mycophenolic acid. Cell 85:921–930. [PubMed][CrossRef]
159. Tiedeman AA, Smith JM. 1985. Nucleotide sequence of the guaB locus encoding IMP dehydrogenase of Escherichia coli K12. Nucleic Acids Res 13:1303–1316. [PubMed][CrossRef]
160. Tesmer JJ, Klem TJ, Deras ML, Davisson VJ, Smith JL. 1996. The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families. Nat Struct Biol 3:74–86. [PubMed][CrossRef]
161. Tiedeman AA, Smith JM, Zalkin H. 1985. Nucleotide sequence of the guaA gene encoding GMP synthetase of Escherichia coli K12. J Biol Chem 260:8676–8679.[PubMed]
162. Zalkin H, Argos P, Narayana SV, Tiedeman AA, Smith JM. 1985. Identification of a trpG-related glutamine amide transfer domain in Escherichia coli GMP synthetase. J Biol Chem 260:3350–3354.[PubMed]
163. Andrews SC, Guest JR. 1988. Nucleotide sequence of the gene encoding the GMP reductase of Escherichia coli K12. Biochem J 255:35–43.[PubMed]
164. Harlow KW, Nygaard P, Hove-Jensen B. 1995. Cloning and characterization of the gsk gene encoding guanosine kinase of Escherichia coli. J Bacteriol 177:2236–2240.[PubMed]
165. Mori H, Iida A, Teshiba S, Fujio T. 1995. Cloning of a guanosine-inosine kinase gene of Escherichia coli and characterization of the purified gene product. J Bacteriol 177:4921–4926.[PubMed]
166. Bennett EM, Li C, Allan PW, Parker WB, Ealick SE. 2003. Structural basis for substrate specificity of Escherichia coli purine nucleoside phosphorylase. J Biol Chem 278:47110–47118. [PubMed][CrossRef]
167. Jensen KF, Nygaard P. 1975. Purine nucleoside phosphorylase from Escherichia coli and Salmonella typhimurium. Purification and some properties Eur J Biochem 51:253–265. [PubMed][CrossRef]
168. Koellner G, Luic M, Shugar D, Saenger W, Bzowska A. 1998. Crystal structure of the ternary complex of E. coli purine nucleoside phosphorylase with formycin B, a structural analogue of the substrate inosine, and phosphate (Sulphate) at 2.1 Å resolution. J Mol Biol 280:153–166. [PubMed][CrossRef]
169. Robertson BC, Hoffee PA. 1973. Purification and properties of purine nucleoside phosphorylase from Salmonella typhimurium. J Biol Chem 248:2040–2043.[PubMed]
170. Dandanell G, Szczepanowski RH, Kierdaszuk B, Shugar D, Bochtler M. 2005. Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene. J Mol Biol 348:113–125. [PubMed][CrossRef]
171. Hammer-Jespersen K, Buxton RS, Hansen TD. 1980. A second purine nucleoside phosphorylase in Escherichia coli K-12. II. Properties of xanthosine phosphorylase and its induction by xanthosine. Mol Gen Genet 179:341–348. [PubMed][CrossRef]
172. Hansen MR, Tranekjaer Jørgensen J, Dandanell G. 2006. Xanthosine utilization in Salmonella enterica serovar Typhimurium is recovered by a single aspartate-to-glycine substitution in xanthosine phosphorylase. J Bacteriol 188:4153–4157. [PubMed][CrossRef]
173. Hansen MR, Dandanell G. 2005. Purification and characterization of RihC, a xanthosine-inosine-uridine-adenosine-preferring hydrolase from Salmonella enterica serovar Typhimurium. Biochim Biophys Acta 1723:55–62.[PubMed]
174. Petersen C, Moller LB. 2001. The RihA, RihB, and RihC ribonucleoside hydrolases of Escherichia coli. Substrate specificity, gene expression, and regulation. J Biol Chem 276:884–894. [PubMed][CrossRef]
175. Maynes JT, Yuan RG, Snyder FF. 2000. Identification, expression, and characterization of Escherichia coli guanine deaminase. J Bacteriol 182:4658–4660. [PubMed][CrossRef]
176. Chang ZY, Nygaard P, Chinault AC, Kellems RE. 1991. Deduced amino acid sequence of Escherichia coli adenosine deaminase reveals evolutionarily conserved amino acid residues: implications for catalytic function. Biochemistry 30:2273–2280. [PubMed][CrossRef]
177. Nygaard P. 1978. Adenosine deaminase from Escherichia coli. Methods Enzymol 51:508–512. [PubMed][CrossRef]
178. Wang Z, Quiocho FA. 1998. Complexes of adenosine deaminase with two potent inhibitors: X-ray structures in four independent molecules at pH of maximum activity. Biochemistry 37:8314–8324. [PubMed][CrossRef]
179. Wilson DK, Quiocho FA. 1994. Crystallographic observation of a trapped tetrahedral intermediate in a metalloenzyme. Nat Struct Biol 1:691–694. [PubMed][CrossRef]
180. Matsui H, Shimaoka M, Kawasaki H, Takenaka Y, Kurahashi O. 2001. Adenine deaminase activity of the yicP gene product of Escherichia coli. Biosci Biotechnol Biochem 65:1112–1118. [PubMed][CrossRef]
181. Petersen C, Moller LB, Valentin-Hansen P. 2002. The cryptic adenine deaminase gene of Escherichia coli. Silencing by the nucleoid-associated DNA-binding protein, H-NS, and activation by insertion elements. J Biol Chem 277:31373–31380. [PubMed][CrossRef]
182. Leung HB, Kvalnes-Krick KL, Meyer SL, deRiel JK, Schramm VL. 1989. Structure and regulation of the AMP nucleosidase gene ( amn) from Escherichia coli. Biochemistry 28:8726–8733. [PubMed][CrossRef]
183. Leung HB, Schramm VL. 1980. Adenylate degradation in Escherichia coli. The role of AMP nucleosidase and properties of the purified enzyme. J Biol Chem 255:10867–10874.[PubMed]
184. Zhang Y, Cottet SE, Ealick SE. 2004. Structure of Escherichia coli AMP nucleosidase reveals similarity to nucleoside phosphorylases. Structure 12:1383–1394. [PubMed][CrossRef]
185. Cornell KA, Riscoe MK. 1998. Cloning and expression of Escherichia coli 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase: identification of the pfs gene product. Biochim Biophys Acta 1396:8–14.[PubMed]
186. Lee JE, Cornell KA, Riscoe MK, Howell PL. 2001. Structure of E. coli 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase reveals similarity to the purine nucleoside phosphorylases. Structure 9:941–953. [PubMed][CrossRef]
187. Lee JE, Cornell KA, Riscoe MK, Howell PL. 2003. Structure of Escherichia coli 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase inhibitor complexes provide insight into the conformational changes required for substrate binding and catalysis. J Biol Chem 278:8761–8770. [PubMed][CrossRef]
188. Lee JE, Singh V, Evans GB, Tyler PC, Furneaux RH, Cornell KA, Riscoe MK, Schramm VL, Howell PL. 2005. Structural rationale for the affinity of pico- and femtomolar transition state analogues of Escherichia coli 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase. J Biol Chem 280:18274–18282. [PubMed][CrossRef]
189. Lohkamp B, McDermott G, Campbell SA, Coggins JR, Lapthorn AJ. 2004. The structure of Escherichia coli ATP-phosphoribosyltransferase: identification of substrate binding sites and mode of AMP inhibition. J Mol Biol 336:131–144. [PubMed][CrossRef]
190. Voll MJ, Appella E, Martin RG. 1967. Purification and composition studies of phosphoribosyladenosine triphosphate:pyrophosphate phosphoribosyltransferase, the first enzyme of histidine biosynthesis. J Biol Chem 242:1760–1767.[PubMed]
191. Houlberg U, Jensen KF. 1983. Role of hypoxanthine and guanine in regulation of Salmonella typhimurium pur gene expression. J Bacteriol 153:837–845.[PubMed]
192. Rolfes RJ, Zalkin H. 1990. Purification of the Escherichia coli purine regulon repressor and identification of corepressors. J Bacteriol 172:5637–5642.[PubMed]
193. Schumacher MA, Choi KY, Lu F, Zalkin H, Brennan RG. 1995. Mechanism of corepressor-mediated specific DNA binding by the purine repressor. Cell 83:147–155. [PubMed][CrossRef]
194. Schumacher MA, Glasfeld A, Zalkin H, Brennan RG. 1997. The X-ray structure of the PurR-guanine- purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity. J Biol Chem 272:22648–22653. [PubMed][CrossRef]
195. Zhou G, Charbonneau H, Colman RF, Zalkin H. 1993. Identification of sites for feedback regulation of glutamine 5-phosphoribosylpyrophosphate amidotransferase by nucleotides and relationship to residues important for catalysis. J Biol Chem 268:10471–10481.[PubMed]
196. Bera AK, Chen S, Smith JL, Zalkin H. 1999. Interdomain signaling in glutamine phosphoribosylpyrophosphate amidotransferase. J Biol Chem 274:36498–36504. [PubMed][CrossRef]
197. Bera AK, Smith JL, Zalkin H. 2000. Dual role for the glutamine phosphoribosylpyrophosphate amidotransferase ammonia channel. Interdomain signaling and intermediate channeling. J Biol Chem 275:7975–7979. [PubMed][CrossRef]
198. Rudolph J, Stubbe J. 1995. Investigation of the mechanism of phosphoribosylamine transfer from glutamine phosphoribosylpyrophosphate amidotransferase to glycinamide ribonucleotide synthetase. Biochemistry 34:2241–2250. [PubMed][CrossRef]
199. Wang W, Kappock TJ, Stubbe J, Ealick SE. 1998. X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli. Biochemistry 37:1564715662. [CrossRef]
200. Dev IK, Harvey RJ. 1978. N10-Formyltetrahydrofolate is the formyl donor for glycinamide ribotide transformylase in Escherichia coli. J Biol Chem 253:4242–4244.[PubMed]
201. Chen P, Schulze-Gahmen U, Stura EA, Inglese J, Johnson DL, Marolewski A, Benkovic SJ, Wilson IA. 1992. Crystal structure of glycinamide ribonucleotide transformylase from Escherichia coli at 3.0 Å resolution. A target enzyme for chemotherapy. J Mol Biol 227:283–392. [PubMed][CrossRef]
202. Inglese J, Smith JM, Benkovic SJ. 1990. Active-site mapping and site-specific mutagenesis of glycinamide ribonucleotide transformylase from Escherichia coli. Biochemistry 29:6678–6687. [PubMed][CrossRef]
203. Nygaard P, Smith JM. 1993. Evidence for a novel glycinamide ribonucleotide transformylase in Escherichia coli. J Bacteriol 175:3591–3597.[PubMed]
204. Marolewski AE, Mattia KM, Warren MS, Benkovic SJ. 1997. Formyl phosphate: a proposed intermediate in the reaction catalyzed by Escherichia coli PurT GAR transformylase. Biochemistry 36:6709–6716. [PubMed][CrossRef]
205. Nagy PL, Marolewski A, Benkovic SJ, Zalkin H. 1995. Formyltetrahydrofolate hydrolase, a regulatory enzyme that functions to balance pools of tetrahydrofolate and one-carbon tetrahydrofolate adducts in Escherichia coli. J Bacteriol 177:1292–1298.[PubMed]
206. Nagy PL, McCorkle GM, Zalkin H. 1993. purU, a source of formate for purT-dependent phosphoribosyl-N-formylglycinamide synthesis. J Bacteriol 175:7066–7073.[PubMed]
207. Dawid IB, French TC, Buchanan JM. 1963. Azaserine-reactive sulfhydryl group of 2-formamido- N-ribosylacetamide 5′-phosphate: L-glutamine amido-ligase (adenosine diphosphate). II. Degradation of azaserine-C-14-labeled enzyme. J Biol Chem 238:2178–2185.[PubMed]
208. Smith JM, Daum HA, III. 1986. Nucleotide sequence of the purM gene encoding 5′-phosphoribosyl-5-aminoimidazole synthetase of Escherichia coli K12. J Biol Chem 261:10632–10636.[PubMed]
209. Mueller EJ, Oh S, Kavalerchik E, Kappock TJ, Meyer E, Li C, Ealick SE, Stubbe J. 1999. Investigation of the ATP binding site of Escherichia coli aminoimidazole ribonucleotide synthetase using affinity labeling and site-directed mutagenesis. Biochemistry 38:9831–9839. [PubMed][CrossRef]
210. Gots JS, Benson CE, Jochimsen B, Koduri KR. 1977. Microbial models and regulatory elements in the control of purine metabolism. Ciba Found Symp 23–41.
211. Tiedeman AA, Keyhani J, Kamholz J, Daum HA, 3rd, Gots JS, Smith JM. 1989. Nucleotide sequence analysis of the purEK operon encoding 5′-phosphoribosyl-5-aminoimidazole carboxylase of Escherichia coli K-12. J Bacteriol 171:205–212.[PubMed]
212. Watanabe W, Sampei G, Aiba A, Mizobuchi K. 1989. Identification and sequence analysis of Escherichia coli purE and purK genes encoding 5′-phosphoribosyl-5-amino-4-imidazole carboxylase for de novo purine biosynthesis. J Bacteriol 171:198–204.[PubMed]
213. Mueller EJ, Meyer E, Rudolph J, Davisson VJ, Stubbe J. 1994. N5-carboxyaminoimidazole ribonucleotide: evidence for a new intermediate and two new enzymatic activities in the de novo purine biosynthetic pathway of Escherichia coli. Biochemistry 33:2269–2278. [PubMed][CrossRef]
214. Firestine SM, Davisson VJ. 1994. Carboxylases in de novo purine biosynthesis. Characterization of the Gallus gallus bifunctional enzyme. Biochemistry 33:11917–11926. [PubMed][CrossRef]
215. Parker J. 1984. Identification of the purC gene product of Escherichia coli. J Bacteriol 157:712–727.[PubMed]
216. Nelson SW, Binkowski DJ, Honzatko RB, Fromm HJ. 2005. Mechanism of action of Escherichia coli phosphoribosylaminoimidazole succinocarboxamide synthetase. Biochemistry 44:766–774. [PubMed][CrossRef]
217. Green SM, Malik T, Giles IG, Drabble WT. 1996. The purB gene of Escherichia coli K-12 is located in an operon. Microbiology 142(Pt 11) :3219–3230. [CrossRef]
218. Gendron N, Breton R, Champagne N, Lapointe J. 1992. Adenylosuccinate lyase of Bacillus subtilis regulates the activity of the glutamyl-tRNA synthetase. Proc Natl Acad Sci USA 89:5389–5392. [PubMed][CrossRef]
219. Hoffman JA, Badger JL, Zhang Y, Kim KS. 2001. Escherichia coli K1 purA and sorC are preferentially expressed upon association with human brain microvascular endothelial cells. Microb Pathog 31:69–79. [PubMed][CrossRef]
220. Gots JS, Dalal FR, Shumas SR. 1969. Genetic separation of the inosinic acid cyclohydrolase-transformylase complex of Salmonella typhimurium. J Bacteriol 99:441–449.[PubMed]
221. Flannigan KA, Hennigan SH, Vogelbacker HH, Gots JS, Smith JM. 1990. Purine biosynthesis in Escherichia coli K12: structure and DNA sequence studies of the purHD locus. Mol Microbiol 4:381–392. [PubMed][CrossRef]
222. Greasley SE, Horton P, Ramcharan J, Beardsley GP, Benkovic SJ, Wilson IA. 2001. Crystal structure of a bifunctional transformylase and cyclohydrolase enzyme in purine biosynthesis. Nat Struct Biol 8:402–406. [PubMed][CrossRef]
223. Wolan DW, Cheong CG, Greasley SE, Wilson IA. 2004. Structural insights into the human and avian IMP cyclohydrolase mechanism via crystal structures with the bound XMP inhibitor. Biochemistry 43:1171–1183. [PubMed][CrossRef]
224. Axelrod HL, McMullan D, Krishna SS, Miller MD, Elsliger MA, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. 2008. Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 Å resolution. Proteins 71:1042–1049. [PubMed][CrossRef]
225. Kilstrup M, Meng LM, Neuhard J, Nygaard P. 1989. Genetic evidence for a repressor of synthesis of cytosine deaminase and purine biosynthesis enzymes in Escherichia coli. J Bacteriol 171:2124–2127.[PubMed]
226. Rolfes RJ, Zalkin H. 1988. Escherichia coli gene purR encoding a repressor protein for purine nucleotide synthesis. Cloning, nucleotide sequence, and interaction with the purF operator. J Biol Chem 263:19653–196561.[PubMed]
227. Meng LM, Kilstrup M, Nygaard P. 1990. Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. Eur J Biochem 187:373–379. [PubMed][CrossRef]
228. Rolfes RJ, Zalkin H. 1990. Autoregulation of Escherichia coli purR requires two control sites downstream of the promoter. J Bacteriol 172:5758–5766.[PubMed]
229. Choi KY, Zalkin H. 1992. Structural characterization and corepressor binding of the Escherichia coli purine repressor. J Bacteriol 174:6207–6914.[PubMed]
230. Huffman JL, Lu F, Zalkin H, Brennan RG. 2002. Role of residue 147 in the gene regulatory function of the Escherichia coli purine repressor. Biochemistry 41:511–520. [PubMed][CrossRef]
231. Arvidson DN, Lu F, Faber C, Zalkin H, Brennan RG. 1998. The structure of PurR mutant L54M shows an alternative route to DNA kinking. Nat Struct Biol 5:436–441. [PubMed][CrossRef]
232. Glasfeld A, Koehler AN, Schumacher MA, Brennan RG. 1999. The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions. J Mol Biol 291:347–361. [PubMed][CrossRef]
233. He B, Zalkin H. 1994. Regulation of Escherichia coli purA by purine repressor, one component of a dual control mechanism. J Bacteriol 176:1009–1013.[PubMed]
234. Lambden PR, Drabble WT. 1973. The gua operon of Escherichia coli K-12: evidence for polarity from guaB to guaA. J Bacteriol 115:992–1002.[PubMed]
235. Tesfa-Selase F, Drabble WT. 1992. Regulation of the gua operon of Escherichia coli by the DnaA protein. Mol Gen Genet 231:256–264.[PubMed]
236. Davies IJ, Drabble WT. 1996. Stringent and growth-rate-dependent control of the gua operon of Escherichia coli K-12. Microbiology 142(Pt 9) :2429–2437. [CrossRef]
237. Husnain SI, Thomas MS. 2008. The UP element is necessary but not sufficient for growth rate-dependent control of the Escherichia coli guaB promoter. J Bacteriol 190:2450–2457. [PubMed][CrossRef]
238. Bass MB, Fromm HJ, Stayton MM. 1987. Overproduction, purification, and characterization of adenylosuccinate synthetase from Escherichia coli. Arch Biochem Biophys 256:335–342. [PubMed][CrossRef]
239. Kang C, Kim S, Fromm HJ. 1996. Subunit complementation of Escherichia coli adenylosuccinate synthetase. J Biol Chem 271:29722–29728. [PubMed][CrossRef]
240. Wang W, Hou Z, Honzatko RB, Fromm HJ. 1997. Relationship of conserved residues in the IMP binding site to substrate recognition and catalysis in Escherichia coli adenylosuccinate synthetase. J Biol Chem 272:16911–16916. [PubMed][CrossRef]
241. Honzatko RB, Fromm HJ. 1999. Structure-function studies of adenylosuccinate synthetase from Escherichia coli. Arch Biochem Biophys 370:1–8. [PubMed][CrossRef]
242. Honzatko RB, Stayton MM, Fromm HJ. 1999. Adenylosuccinate synthetase: recent developments. Adv Enzymol Relat Areas Mol Biol 73:57–102. [PubMed][CrossRef]
243. Bass MB, Fromm HJ, Rudolph FB. 1984. The mechanism of the adenylosuccinate synthetase reaction as studied by positional isotope exchange. J Biol Chem 259:12330–12333.[PubMed]
244. Choe JY, Poland BW, Fromm HJ, Honzatko RB. 1999. Mechanistic implications from crystalline complexes of wild-type and mutant adenylosuccinate synthetases from Escherichia coli. Biochemistry 38:6953–6961. [PubMed][CrossRef]
245. Poland BW, Bruns C, Fromm HJ, Honzatko RB. 1997. Entrapment of 6-thiophosphoryl-IMP in the active site of crystalline adenylosuccinate synthetase from Escherichia coli. J Biol Chem 272:15200–15205. [PubMed][CrossRef]
246. Cashel M, Gallant J. 1969. Two compounds implicated in the function of the RC gene of Escherichia coli. Nature 221:838–841. [PubMed][CrossRef]
247. Hou Z, Cashel M, Fromm HJ, Honzatko RB. 1999. Effectors of the stringent response target the active site of Escherichia coli adenylosuccinate synthetase. J Biol Chem 274:17505–17510. [PubMed][CrossRef]
248. Oshchepkova-Nedosekina EA, Likhoshvai VA. 2007. A mathematical model for the adenylosuccinate synthetase reaction involved in purine biosynthesis. Theor Biol Med Model 4:11. [CrossRef]
249. Buzzee DH, Levin AP. 1968. Demonstration of an effector site for the enzyme inosine 5′-phosphate dehydrogenase. Biochem Biophys Res Commun 30:673–677. [PubMed][CrossRef]
250. Gilbert HJ, Lowe CR, Drabble WT. 1979. Inosine 5′-monophosphate dehydrogenase of Escherichia coli. Purification by affinity chromatography, subunit structure and inhibition by guanosine 5′-monophosphate. Biochem J 183:481–494.[PubMed]
251. Guillen Schlippe YV, Hedstrom L. 2005. Is Arg418 the catalytic base required for the hydrolysis step of the IMP dehydrogenase reaction? Biochemistry 44:11700–11707. [PubMed][CrossRef]
252. Hedstrom L. 1999. IMP dehydrogenase: mechanism of action and inhibition. Curr Med Chem 6:545–560.[PubMed]
253. Kerr KM, Digits JA, Kuperwasser N, Hedstrom L. 2000. Asp338 controls hydride transfer in Escherichia coli IMP dehydrogenase. Biochemistry 39:9804–9810. [PubMed][CrossRef]
254. Ignoul S, Eggermont J. 2005. CBS domains: structure, function, and pathology in human proteins. Am J Physiol 289:C1369–C1378. [CrossRef]
255. Nimmesgern E, Black J, Futer O, Fulghum JR, Chambers SP, Brummel CL, Raybuck SA, Sintchak MD. 1999. Biochemical analysis of the modular enzyme inosine 5′-monophosphate dehydrogenase. Protein Expr Purif 17:282–289. [PubMed][CrossRef]
256. Mortimer SE, Hedstrom L. 2005. Autosomal dominant retinitis pigmentosa mutations in inosine 5′-monophosphate dehydrogenase type I disrupt nucleic acid binding. Biochem J 390:41–47. [PubMed][CrossRef]
257. Scott JW, Hawley SA, Green KA, Anis M, Stewart G, Scullion GA, Norman DG, Hardie DG. 2004. CBS domains form energy-sensing modules whose binding of adenosine ligands is disrupted by disease mutations. J Clin Invest 113:274–284. [PubMed][CrossRef]
258. McLean JE, Hamaguchi N, Belenky P, Mortimer SE, Stanton M, Hedstrom L. 2004. Inosine 5′-monophosphate dehydrogenase binds nucleic acids in vitro and in vivo. Biochem J 379:243–251. [PubMed][CrossRef]
259. Pimkin M, Markham GD. 2008. The CBS subdomain of inosine 5′-monophosphate dehydrogenase regulates purine nucleotide turnover. Mol. Microbiol. 68:342–359. [CrossRef]
260. Zalkin H. 1985. GMP synthetase. Methods Enzymol 113:273–278. [PubMed][CrossRef]
261. Zalkin H, Truitt CD. 1977. Characterization of the glutamine site of Escherichia coli guanosine 5′-monophosphate synthetase. J Biol Chem 252:5431–5436.[PubMed]
262. von der Saal W, Crysler CS, Villafranca JJ. 1985. Positional isotope exchange and kinetic experiments with Escherichia coli guanosine-5′-monophosphate synthetase. Biochemistry 24:5343–5350. [PubMed][CrossRef]
263. Sakamoto N, Hatfield GW, Moyed HS. 1972. Denaturation and renaturation of xanthosine 5′-phosphate aminase. J Biol Chem 247:5888–5891.[PubMed]
264. Sakamoto N, Hatfield GW, Moyed HS. 1972. Physical properties and subunit structure of xanthosine 5′-phosphate aminase. J Biol Chem 247:5880–5887.[PubMed]
265. Karlström HO. 1970. Inability of Escherichia coli B to incorporate added deoxycytidine, deoxyandenosine, and deoxyguanosine into DNA. Eur J Biochem 17:68–71. [PubMed][CrossRef]
266. Nygaard P. 1983. Purine salvage pathways, p 27–93. In Munch-Petersen A (ed), Metabolism of Nucleotides, Nucleosides and Nucleobases in Microorganisms. Academic Press, London, United Kingdom.
267. Jensen KF. 1976. Purine-nucleoside phosphorylase from Salmonella typhimurium and Escherichia coli. Initial velocity kinetics, ligand banding, and reaction mechanism. Eur J Biochem 61:377–386. [PubMed][CrossRef]
268. Hammer-Jespersen K, Munch-Petersen A, Schwartz M, Nygaard P. 1971. Induction of enzymes involed in the catabolism of deoxyribonucleosides and ribonucleosides in Escherichia coli K 12. Eur J Biochem 19:533–538. [PubMed][CrossRef]
269. Valentin-Hansen P, Hammer K, Love Larsen JE, Svendsen I. 1984. The internal regulated promoter of the deo operon of Escherichia coli K-12. Nucleic Acids Res 12:5211–5224. [PubMed][CrossRef]
270. Buxton RS, Hammer-Jespersen K, Valentin-Hansen P. 1980. A second purine nucleoside phosphorylase in Escherichia coli K-12. I. Xanthosine phosphorylase regulatory mutants isolated as secondary-site revertants of a deoD mutant. Mol Gen Genet 179:331–340. [PubMed][CrossRef]
271. Seeger C, Poulsen C, Dandanell G. 1995. Identification and characterization of genes ( xapA, xapB, and xapR) involved in xanthosine catabolism in Escherichia coli. J Bacteriol 177:5506–5516.[PubMed]
272. Jensen KF. 1989. Regulation of Salmonella typhimurium pyr gene expression: effect of changing both purine and pyrimidine nucleotide pools. J Gen Microbiol 135:805–815.[PubMed]
273. Mager J, Magasnik B. 1960. Guanosine 5′-phosphate reductase and its role in the interconversion of purine nucleotides. J Biol Chem 235:1474–1478.[PubMed]
274. Kessler AI, Gots JS. 1985. Regulation of guaC expression in Escherichia coli. J Bacteriol 164:1288–1293.[PubMed]
275. Benson CE, Gots JS. 1975. Regulation of GMP reductase in Salmonella typhimurium. Biochim Biophys Acta 403:47–57.[PubMed]
276. Kawasaki H, Shimaoka M, Usuda Y, Utagawa T. 2000. End-product regulation and kinetic mechanism of guanosine-inosine kinase from Escherichia coli. Biosci Biotechnol Biochem 64:972–979. [PubMed][CrossRef]
277. Petersen C. 1999. Inhibition of cellular growth by increased guanine nucleotide pools. Characterization of an Escherichia coli mutant with a guanosine kinase that is insensitive to feedback inhibition by GTP. J Biol Chem 274:5348–5356. [PubMed][CrossRef]
278. Kierdaszuk B, Modrak-Wojcik A, Shugar D. 1997. Binding of phosphate and sulfate anions by purine nucleoside phosphorylase from E. coli: ligand-dependent quenching of enzyme intrinsic fluorescence Biophys Chem 63:107–118. [PubMed][CrossRef]
279. Fedorov A, Shi W, Kicska G, Fedorov E, Tyler PC, Furneaux RH, Hanson JC, Gainsford GJ, Larese JZ, Schramm VL, Almo SC. 2001. Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis. Biochemistry 40:853–860. [PubMed][CrossRef]
280. Kline PC, Schramm VL. 1995. Pre-steady-state transition-state analysis of the hydrolytic reaction catalyzed by purine nucleoside phosphorylase. Biochemistry 34:1153–1162. [PubMed][CrossRef]
281. Pugmire MJ, Ealick SE. 2002. Structural analyses reveal two distinct families of nucleoside phosphorylases. Biochem J 361:1–25. [PubMed][CrossRef]
282. Rinaldo-Matthis A, Wing C, Ghanem M, Deng H, Wu P, Gupta A, Tyler PC, Evans GB, Furneaux RH, Almo SC, Wang CC, Schramm VL. 2007. Inhibition and structure of Trichomonas vaginalis purine nucleoside phosphorylase with picomolar transition state analogues. Biochemistry 46:659–668. [PubMed][CrossRef]
283. Koszalka GW, Vanhooke J, Short SA, Hall WW. 1988. Purification and properties of inosine-guanosine phosphorylase from Escherichia coli K-12. J Bacteriol 170:3493–3498.[PubMed]
284. Mao C, Cook WJ, Zhou M, Koszalka GW, Krenitsky TA, Ealick SE. 1997. The crystal structure of Escherichia coli purine nucleoside phosphorylase: a comparison with the human enzyme reveals a conserved topology. Structure 5:1373–1383. [PubMed][CrossRef]
285. Modrak-Wojcik A, Kirilenko A, Shugar D, Kierdaszuk B. 2008. Role of ionization of the phosphate cosubstrate on phosphorolysis by purine nucleoside phosphorylase (PNP) of bacterial ( E. coli) and mammalian (human) origin. Eur Biophys J 37:153–164. [PubMed][CrossRef]
286. Stoychev G, Kierdaszuk B, Shugar D. 2002. Xanthosine and xanthine. Substrate properties with purine nucleoside phosphorylases, and relevance to other enzyme systems. Eur J Biochem 269:4048–4057. [PubMed][CrossRef]
287. Hunt C, Gillani N, Farone A, Rezaei M, Kline PC. 2005. Kinetic isotope effects of nucleoside hydrolase from Escherichia coli. Biochim Biophys Acta 1751:140–149.[PubMed]
288. Deo SS, Tseng WC, Saini R, Coles RS, Athwal RS. 1985. Purification and characterization of Escherichia coli xanthine-guanine phosphoribosyltransferase produced by plasmid pSV2gpt. Biochim Biophys Acta 839:233–239.[PubMed]
289. Hochstadt J. 1978. Hypoxanthine phosphoribosyltransferase and guanine phosphoribosyltransferase from enteric bacteria. Methods Enzymol 51:549–558. [PubMed][CrossRef]
290. Meng LM, Nygaard P. 1990. Identification of hypoxanthine and guanine as the co-repressors for the purine regulon genes of Escherichia coli. Mol Microbiol 4:2187–2192. [PubMed][CrossRef]
291. Levine RA, Taylor MW. 1982. Mechanism of adenine toxicity in Escherichia coli. J Bacteriol 149:923–930.[PubMed]
292. Arent S, Kadziola A, Larsen S, Neuhard J, Jensen KF. 2006. The extraordinary specificity of xanthine phosphoribosyltransferase from Bacillus subtilis elucidated by reaction kinetics, ligand binding, and crystallography. Biochemistry 45:6615–6627. [PubMed][CrossRef]
293. Goudela S, Karatza P, Koukaki M, Frillingos S, Diallinas G. 2005. Comparative substrate recognition by bacterial and fungal purine transporters of the NAT/NCS2 family. Mol Membr Biol 22:263–275. [PubMed][CrossRef]
294. Karatza P, Frillingos S. 2005. Cloning and functional characterization of two bacterial members of the NAT/NCS2 family in Escherichia coli. Mol Membr Biol 22:251–261. [PubMed][CrossRef]
295. Karatza P, Panos P, Georgopoulou E, Frillingos S. 2006. Cysteine-scanning analysis of the nucleobase-ascorbate transporter signature motif in YgfO permease of Escherichia coli: Gln-324 and Asn-325 are essential, and Ile-329-Val-339 form an alpha-helix. J Biol Chem 281:39881–39890. [PubMed][CrossRef]
296. Xi H, Schneider BL, Reitzer L. 2000. Purine catabolism in Escherichia coli and function of xanthine dehydrogenase in purine salvage. J Bacteriol 182:5332–5341. [PubMed][CrossRef]
297. Carter CW, Jr. 1995. The nucleoside deaminases for cytidine and adenosine: structure, transition state stabilization, mechanism, and evolution. Biochimie 77:92–98. [PubMed][CrossRef]
298. Ames BN, Martin RG, Garry BJ. 1961. The first step of histidine biosynthesis. J Biol Chem 236:2019–2026.[PubMed]
299. Morton DP, Parsons SM. 1977. Synergistic inhibition of ATP phosphoribosyltransferase by guanosine tetraphosphate and histidine. Biochem Biophys Res Commun 74:172–177. [PubMed][CrossRef]
300. Barnes WM. 1978. DNA sequence from the histidine operon control region: seven histidine codons in a row. Proc Natl Acad Sci USA 75:4281–4285. [PubMed][CrossRef]
301. Carlomagno MS, Chiariotti L, Alifano P, Nappo AG, Bruni CB. 1988. Structure and function of the Salmonella typhimurium and Escherichia coli K-12 histidine operons. J Mol Biol 203:585–606. [PubMed][CrossRef]
302. Leung HB, Schramm VL. 1984. The structural gene for AMP nucleosidase. Mapping, cloning, and overproduction of the enzyme. J Biol Chem 259:6972–6978.[PubMed]
303. Baek JH, Lee SY. 2006. Novel gene members in the Pho regulon of Escherichia coli. FEMS Microbiol Lett 264:104–109. [PubMed][CrossRef]
304. Morrison BA, Shain DH. 2008. An AMP nucleosidase gene knockout in Escherichia coli elevates intracellular ATP levels and increases cold tolerance. Biol Lett 4:53–56. [PubMed][CrossRef]
305. Cornell KA, Swarts WE, Barry RD, Riscoe MK. 1996. Characterization of recombinant Eschericha coli 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase: analysis of enzymatic activity and substrate specificity. Biochem Biophys Res Commun 228:724–732. [PubMed][CrossRef]
306. Cornell KA, Winter RW, Tower PA, Riscoe MK. 1996. Affinity purification of 5-methylthioribose kinase and 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Klebsiella pneumoniae. Biochem J 317(Pt 1) :285–290.
307. Lee JE, Cornell KA, Riscoe MK, Howell PL. 2001. Expression, purification, crystallization and preliminary X-ray analysis of Escherichia coli 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase. Acta Crystallogr D Biol Crystallogr 57:150–152. [PubMed][CrossRef]
308. Gutierrez JA, Luo M, Singh V, Li L, Brown RL, Norris GE, Evans GB, Furneaux RH, Tyler PC, Painter GF, Lenz DH, Schramm VL. 2007. Picomolar inhibitors as transition-state probes of 5′-methylthioadenosine nucleosidases. ACS Chem Biol 2:725–734. [PubMed][CrossRef]
309. Singh V, Evans GB, Lenz DH, Mason JM, Clinch K, Mee S, Painter GF, Tyler PC, Furneaux RH, Lee JE, Howell PL, Schramm VL. 2005. Femtomolar transition state analogue inhibitors of 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Escherichia coli. J Biol Chem 280:18265–18273. [PubMed][CrossRef]
310. Appleby TC, Erion MD, Ealick SE. 1999. The structure of human 5′-deoxy-5′-methylthioadenosine phosphorylase at 1.7 Å resolution provides insights into substrate binding and catalysis. Structure 7:629–641. [PubMed][CrossRef]
311. Appleby TC, Mathews II, Porcelli M, Cacciapuoti G, Ealick SE. 2001. Three-dimensional structure of a hyperthermophilic 5′-deoxy-5′-methylthioadenosine phosphorylase from Sulfolobus solfataricus. J Biol Chem 276:39232–29242. [PubMed][CrossRef]
312. Pierard A. 1966. Control of the activity of Escherichia coli carbamoyl phosphate synthetase by antagonistic allosteric effectors. Science 154:1572–1573. [PubMed][CrossRef]
313. Abdelal AT, Ingraham JL. 1975. Carbamylphosphate synthetase from Salmonella typhimurium. Regulations, subunit composition, and function of the subunits. J Biol Chem 250:4410–4417.[PubMed]
314. Boettcher B, Meister A. 1982. Regulation of Escherichia coli carbamyl phosphate synthetase. Evidence for overlap of the allosteric nucleotide binding sites. J Biol Chem 257:13971–13976.[PubMed]
315. Mergeay M, Gigot D, Beckmann J, Glansdorff N, Pierard A. 1974. Physiology and genetics of carbamoylphosphate synthesis in Escherichia coli K12. Mol Gen Genet 133:299–316. [PubMed][CrossRef]
316. Trotta PP, Estis LF, Meister A, Haschemeyer RH. 1974. Self-association and allosteric properties of glutamine-dependent carbamyl phosphate synthetase. Reversible dissociation to monomeric species. J Biol Chem 249:482–489.[PubMed]
317. Trotta PP, Pinkus LM, Haschemeyer RH, Meister A. 1974. Reversible dissociation of the monomer of glutamine-dependent carbamyl phosphate synthetase into catalytically active heavy and light subunits. J Biol Chem 249:492–499.[PubMed]
318. Anderson PM. 1977. Evidence that the catalytic and regulatory functions of carbamylphosphate synthetase from Escherichia coli are not dependent on oligomer formation. Biochemistry 16:583–586. [PubMed][CrossRef]
319. Holden HM, Thoden JB, Raushel FM. 1999. Carbamoyl phosphate synthetase: an amazing biochemical odyssey from substrate to product. Cell Mol Life Sci 56:507–522. [PubMed][CrossRef]
320. Raushel FM, Thoden JB, Reinhart GD, Holden HM. 1998. Carbamoyl phosphate synthetase: a crooked path from substrates to products. Curr Opin Chem Biol 2:624–632. [PubMed][CrossRef]
321. Thoden JB, Wesenberg G, Raushel FM, Holden HM. 1999. Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding. Biochemistry 38:2347–2357. [PubMed][CrossRef]
322. Thoden JB, Raushel FM, Wesenberg G, Holden HM. 1999. The binding of inosine monophosphate to Escherichia coli carbamoyl phosphate synthetase. J Biol Chem 274:22502–22507. [PubMed][CrossRef]
323. Thoden JB, Huang X, Kim J, Raushel FM, Holden HM. 2004. Long-range allosteric transitions in carbamoyl phosphate synthetase. Protein Sci 13:2398–2405. [PubMed][CrossRef]
324. England P, Leconte C, Tauc P, Herve G. 1994. Apparent cooperativity for carbamoylphosphate in Escherichia coli aspartate transcarbamoylase only reflects cooperativity for aspartate. Eur J Biochem 222:775–780. [PubMed][CrossRef]
325. England P, Herve G. 1994. Involvement of the gamma-phosphate of UTP in the synergistic inhibition of Escherichia coli aspartate transcarbamylase by CTP and UTP. Biochemistry 33:3913–3918. [PubMed][CrossRef]
326. England P, Herve G. 1992. Synergistic inhibition of Escherichia coli aspartate transcarbamylase by CTP and UTP: binding studies using continuous-flow dialysis. Biochemistry 31:9725–9732. [PubMed][CrossRef]
327. Wild JR, Loughrey-Chen SJ, Corder TS. 1989. In the presence of CTP, UTP becomes an allosteric inhibitor of aspartate transcarbamoylase. Proc Natl Acad Sci USA 86:46–50. [PubMed][CrossRef]
328. Zhang Y, Kantrowitz ER. 1991. The synergistic inhibition of Escherichia coli aspartate carbamoyltransferase by UTP in the presence of CTP is due to the binding of UTP to the low affinity CTP sites. J Biol Chem 266:22154–22158.[PubMed]
329. Bothwell M, Schachman HK. 1974. Pathways of assembly of aspartate transcarbamoylase from catalytic and regulatory subunits. Proc Natl Acad Sci USA 71:3221–3225. [PubMed][CrossRef]
330. Gerhart JC, Schachman HK. 1965. Distinct subunits for the regulation and catalytic activity of aspartate transcarbamylase. Biochemistry 4:1054–1062. [PubMed][CrossRef]
331. Markby DW, Zhou BB, Schachman HK. 1991. A 70-amino acid zinc-binding polypeptide from the regulatory chain of aspartate transcarbamoylase forms a stable complex with the catalytic subunit leading to markedly altered enzyme activity. Proc Natl Acad Sci USA 88:10568–10572. [PubMed][CrossRef]
332. McCarthy MP, Allewell NM. 1983. Thermodynamics of assembly of Escherichia coli aspartate transcarbamoylase. Proc Natl Acad Sci USA 80:6824–6828. [PubMed][CrossRef]
333. Nelbach ME, Pigiet VP, Jr, Gerhart JC, Schachman HK. 1972. A role for zinc in the quaternary structure of aspartate transcarbamylase from Escherichia coli. Biochemistry 11:315–327. [PubMed][CrossRef]
334. Wang J, Stieglitz KA, Cardia JP, Kantrowitz ER. 2005. Structural basis for ordered substrate binding and cooperativity in aspartate transcarbamoylase. Proc Natl Acad Sci USA 102:8881–8886. [PubMed][CrossRef]
335. Gerhart JC, Schachman HK. 1968. Allosteric interactions in aspartate transcarbamylase. II. Evidence for different conformational states of the protein in the presence and absence of specific ligands. Biochemistry 7:538–552. [PubMed][CrossRef]
336. Howlett GJ, Blackburn MN, Compton JG, Schachman HK. 1977. Allosteric regulation of aspartate transcarbamoylase. Analysis of the structural and functional behavior in terms of a two-state model. Biochemistry 16:5091–5100. [PubMed][CrossRef]
337. Howlett GJ, Schachman HK. 1977. Allosteric regulation of aspartate transcarbamoylase. Changes in the sedimentation coefficient promoted by the bisubstrate analogue N-(phosphonacetyl)- L-aspartate. Biochemistry 16:5077–5083. [PubMed][CrossRef]
338. Monod J, Wyman J, Changeux J-P. 1965. On the nature of allosteric transitions: a plausible model. J Mol Biol 12:88–118. [PubMed][CrossRef]
339. Fetler L, Tauc P, Herve G, Moody MF, Vachette P. 1995. X-ray scattering titration of the quaternary structure transition of aspartate transcarbamylase with a bisubstrate analogue: influence of nucleotide effectors. J Mol Biol 251:243–255. [PubMed][CrossRef]
340. Stieglitz K, Stec B, Baker DP, Kantrowitz ER. 2004. Monitoring the transition from the T to the R state in E. coli aspartate transcarbamoylase by X-ray crystallography: crystal structures of the E50A mutant enzyme in four distinct allosteric states. J Mol Biol 341:853–868. [PubMed][CrossRef]
341. Stieglitz KA, Dusinberre KJ, Cardia JP, Tsuruta H, Kantrowitz ER. 2005. Structure of the E. coli aspartate transcarbamoylase trapped in the middle of the catalytic cycle. J Mol Biol 352:478–486. [PubMed][CrossRef]
342. Stieglitz KA, Pastra-Landis SC, Xia J, Tsuruta H, Kantrowitz ER. 2005. A single amino acid substitution in the active site of Escherichia coli aspartate transcarbamoylase prevents the allosteric transition. J Mol Biol 349:413–423. [PubMed][CrossRef]
343. Wang J, Eldo J, Kantrowitz ER. 2007. Structural model of the R state of Escherichia coli aspartate transcarbamoylase with substrates bound. J Mol Biol 371:1261–1273. [PubMed][CrossRef]
344. West JM, Kantrowitz ER. 2003. Trapping specific quaternary states of the allosteric enzyme aspartate transcarbamoylase in silica matrix sol-gels. J Am Chem Soc 125:9924–9925. [PubMed][CrossRef]
345. West JM, Tsuruta H, Kantrowitz ER. 2004. A fluorescent probe-labeled Escherichia coli aspartate transcarbamoylase that monitors the allosteric conformational state. J Biol Chem 279:945–951. [PubMed][CrossRef]
346. West JM, Tsuruta H, Kantrowitz ER. 2002. Stabilization of the R allosteric structure of Escherichia coli aspartate transcarbamoylase by disulfide bond formation. J Biol Chem 277:47300–47304. [PubMed][CrossRef]
347. Fetler L, Vachette P. 2002. Revisiting the allosteric mechanism of aspartate transcarbamoylase. Nat Struct Biol 9:87–89. [PubMed][CrossRef]
348. Macol CP, Tsuruta H, Stec B, Kantrowitz ER. 2001. Direct structural evidence for a concerted allosteric transition in Escherichia coli aspartate transcarbamoylase. Nat Struct Biol 8:423–426. [PubMed][CrossRef]
349. Gerhart JC. 1970. A discussion of the regulatory properties of aspartate transcarbamylase from Escherichia coli. Curr Top Cell Regul 2:275–325.
350. Huang J, Lipscomb WN. 2006. T-state active site of aspartate transcarbamylase: crystal structure of the carbamyl phosphate and L-alanosine ligated enzyme. Biochemistry 45:346–352. [PubMed][CrossRef]
351. Kantrowitz ER, Lipscomb WN. 1990. Escherichia coli aspartate transcarbamoylase: the molecular basis for a concerted allosteric transition. Trends Biochem Sci 15:53–59. [PubMed][CrossRef]
352. Schachman HK. 1988. Can a simple model account for the allosteric transition of aspartate transcarbamoylase? J Biol Chem 263:18583–18586.[PubMed]
353. Bäckström D, Sjöberg RM, Lundberg LG. 1986. Nucleotide sequence of the structural gene for dihydroorotase of Escherichia coli K12. Eur J Biochem 160:77–82. [PubMed][CrossRef]
354. Neuhard J, Kelln RA, Stauning E. 1986. Cloning and structural characterization of the Salmonella typhimurium pyrC gene encoding dihydroorotase. Eur J Biochem 157:335–342. [PubMed][CrossRef]
355. Wilson HR, Chan PT, Turnbough CL, Jr. 1987. Nucleotide sequence and expression of the pyrC gene of Escherichia coli K-12. J Bacteriol 169:3051–3058.[PubMed]
356. Brown DC, Collins KD. 1991. Dihydroorotase from Escherichia coli. Substitution of Co(II) for the active site Zn(II). J Biol Chem 266:1597–1604.[PubMed]
357. Thoden JB, Phillips GN, Jr, Neal TM, Raushel FM, Holden HM. 2001. Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center. Biochemistry 40:6989–6997. [PubMed][CrossRef]
358. Washabaugh MW, Collins KD. 1984. Dihydroorotase from Escherichia coli. Purification and characterization. J Biol Chem 259:3293–3298.[PubMed]
359. Washabaugh MW, Collins KD. 1986. Dihydroorotase from Escherichia coli. Sulfhydryl group-metal ion interactions. J Biol Chem 261:5920–5929.[PubMed]
360. Lee M, Chan CW, Mitchell Guss J, Christopherson RI, Maher MJ. 2005. Dihydroorotase from Escherichia coli: loop movement and cooperativity between subunits. J Mol Biol 348:523–533. [PubMed][CrossRef]
361. Lee M, Maher MJ, Christopherson RI, Guss JM. 2007. Kinetic and structural analysis of mutant Escherichia coli dihydroorotases: a flexible loop stabilizes the transition state. Biochemistry 46:10538–10550. [PubMed][CrossRef]
362. Lee M, Maher MJ, Guss JM. 2007. Structure of the T109S mutant of Escherichia coli dihydroorotase complexed with the inhibitor 5-fluoroorotate: catalytic activity is reflected by the crystal form. Acta Crystallogr Sect F Struct Biol Cryst Commun 63:154–161. [PubMed][CrossRef]
363. Lee M, Chan CW, Graham SC, Christopherson RI, Guss JM, Maher MJ. 2007. Structures of ligand-free and inhibitor complexes of dihydroorotase from Escherichia coli: implications for loop movement in inhibitor design. J Mol Biol 370:812–825. [PubMed][CrossRef]
364. Jensen KF. 2002. The divergent family of dihydroorotate dehydrogenases, p 481–490. In Chapman S, Perham R, and Scrutton N (ed), Flavins and Flavoproteins 2002. Rudolf Weber, Agency for Scientific Publications, Berlin, Germany.
365. Jensen KF, Björnberg O. 1998. Evolutionary and functional families of dihydroorotate dehydrogenases. Paths to Pyrimidines 6(1) :20–28.
366. Rowland P, Nielsen FS, Jensen KF, Larsen S. 1997. The crystal structure of the flavin containing enzyme dihydroorotate dehydrogenase A from Lactococcus lactis. Structure 5:239–250. [PubMed][CrossRef]
367. Andrews S, Cox GB, Gibson F. 1977. The anaerobic oxidation of dihydroorotate by Escherichia coli K-12. Biochim Biophys Acta 462:153–160. [PubMed][CrossRef]
368. Kerr CT, Miller RW. 1968. Dihydroorotate-ubiquinone reductase complex of Escherichia coli B. J Biol Chem 243:2963–2968.[PubMed]
369. Karibian D. 1978. Dihydroorotate dehydrogenase ( Escherichia coli). Methods Enzymol 51:58–63. [PubMed][CrossRef]
370. Karibian D, Couchoud P. 1974. Dihydro-orotate oxidase of Escherichia coli K12: purification, properties, and relation to the cytoplasmic membrane. Biochim Biophys Acta 364:218–232.[PubMed]
371. Larsen JN, Jensen KF. 1985. Nucleotide sequence of the pyrD gene of Escherichia coli and characterization of the flavoprotein dihydroorotate dehydrogenase. Eur J Biochem 151:59–65. [PubMed][CrossRef]
372. Björnberg O, Grüner AC, Roepstorff P, Jensen KF. 1999. The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology, mutagenesis and limited proteolysis. Biochemistry 28:2899–2908. [CrossRef]
373. Shi J, Palfey BA, Dertouzos J, Jensen KF, Gafni A, Steel D. 2004. Multiple states of the Tyr318Leu mutant of dihydroorotate dehydrogenase revealed by single-molecule kinetics. J Am Chem Soc 126:6914–6922. [PubMed][CrossRef]
374. Nielsen FS, Andersen PS, Jensen KF. 1996. The B-form of dihydroorotate dehydrogenase from Lactococcus lactis consists of two different subunits, encoded by the pyrDb and pyrK genes, and contains FMN, FAD, and [FeS] redox centres. J Biol Chem 271:29359–29365. [PubMed][CrossRef]
375. Nielsen FS, Rowland P, Larsen S, Jensen KF. 1996. Purification and characterization of dihydroorotate dehydrogenase A from Lactococcus lactis, crystallization and preliminary X-ray diffraction studies of the enzyme. Protein Sci 5:857–861.[PubMed]
376. Rowland P, Nørager S, Jensen KF, Larsen S. 2000. Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster. Structure 8:1227–1238. [PubMed][CrossRef]
377. Nørager S, Jensen KF, Björnberg O, Larsen S. 2002. E. coli dihydroorotate dehydrogenase reveals structural and functional differences between different classes of dihydroorotate dehydrogenases. Structure 10:1211–1233. [PubMed][CrossRef]
378. Björnberg O, Jordan DB, Palfey BA, Jensen KF. 2001. Dihydrooxonate is a substrate of dihydroorotate dehydrogenase (DHOD) providing evidence for involvement of cysteine and serine residues in base catalysis. Arch Biochem Biophys 391:286–294. [PubMed][CrossRef]
379. Fagan RL, Nelson MN, Pagano PM, Palfey BA. 2006. Mechanism of flavin reduction in class 2 dihydroorotate dehydrogenases. Biochemistry 45:14926–14932. [PubMed][CrossRef]
380. Couto SG, Nonato MC, Costa-Filho AJ. 2007. Defects in vesicle core induced by Escherichia coli DHODH. Biophys J 94:1746–1753. [PubMed][CrossRef]
381. Liu S, Neidhardt EA, Grossman TH, Ocain T, Clardy J. 2000. Structures of human dihydroorotate dehydrogenase in complex with antiproliferative agents. Structure 8:25–33. [PubMed][CrossRef]
382. Löffler M, Knecht W, Rawls J, Ullrich A, Dietz C. 2002. Drosophila melanogaster dihydroorotate dehydrogenase: the N-terminus is important for biological function in vivo but not for catalytic properties in vitro. Insect Biochem Mol Biol 32:1159–1169. [PubMed][CrossRef]
383. Rawls J, Knecht W, Diekert K, Lill R, Löffler M. 2000. Requirements for the mitochondrial import and localization of dihydroorotate dehydrogenase. Eur J Biochem 267:2079–2087. [PubMed][CrossRef]
384. Scapin G, Sacchettini JC, Dessen A, Bhatia M, Grubmeyer C. 1993. Primary structure and crystallization of orotate phosphoribosyltransferase from Salmonella typhimurium. J Mol Biol 230:1304–1308. [PubMed][CrossRef]
385. Bhatia MB, Grubmeyer C. 1993. The role of divalent magnesium in activating the reaction catalyzed by orotate phosphoribosyltransferase. Arch Biochem Biophys 303:321–325. [PubMed][CrossRef]
386. Bhatia MB, Vinitsky A, Grubmeyer C. 1990. Kinetic mechanism of orotate phosphoribosyltransferase from Salmonella typhimurium. Biochemistry 29:10480–10487. [PubMed][CrossRef]
387. Tao W, Grubmeyer C, Blanchard JS. 1996. Transition state structure of Salmonella typhimurium orotate phosphoribosyltransferase. Biochemistry 35:14–21. [PubMed][CrossRef]
388. Wang GP, Lundegaard C, Jensen KF, Grubmeyer C. 1999. Kinetic mechanism of OMP synthase: a slow physical step following group transfer limits catalytic rate. Biochemistry 38:275–283. [PubMed][CrossRef]
389. Wang GP, Cahill SM, Liu X, Girvin ME, Grubmeyer C. 1999. Motional dynamics of the catalytic loop in OMP synthase. Biochemistry 38:284–295. [PubMed][CrossRef]
390. Ozturk DH, Dorfman RH, Scapin G, Sacchettini JC, Grubmeyer C. 1995. Locations and functional roles of conserved lysine residues in Salmonella typhimurium orotate phosphoribosyltransferase. Biochemistry 34:10755–10763. [PubMed][CrossRef]
391. Ozturk DH, Dorfman RH, Scapin G, Sacchettini JC, Grubmeyer C. 1995. Structure and function of Salmonella typhimurium orotate phosphoribosyltransferase: protein complementation reveals shared active sites. Biochemistry 34:10764–10770. [PubMed][CrossRef]
392. Gonzalez-Segura L, Witte JF, McClard RW, Hurley TD. 2007. Ternary complex formation and induced asymmetry in orotate phosphoribosyltransferase. Biochemistry 46:14075–14086. [PubMed][CrossRef]
393. McClard RW, Holets EA, MacKinnon AL, Witte JF. 2006. Half-of-sites binding of orotidine 5′-phosphate and α- D-5-phosphoribose 1-diphosphate to orotate phosphoribosyltransferase from Saccharomyces cerevisiae supports a novel variant of the Theorell-Chance mechanism with alternating site catalysis. Biochemistry 45:5330–5342. [PubMed][CrossRef]
394. Theisen M, Kelln RA, Neuhard J. 1987. Cloning and characterization of the pyrF operon of Salmonella typhimurium. Eur J Biochem 164:613–619. [PubMed][CrossRef]
395. Turnbough CL Jr, Kerr KH, Funderburg WR, Donahue JP, Powell FE. 1987. Nucleotide sequence and characterization of the pyrF operon of Escherichia coli K12. J Biol Chem 262:10239–10245.[PubMed]
396. Jensen KF, Larsen JN, Schack L, Sivertsen A. 1984. Studies on the structure and expression of Escherichia coli pyrC, pyrD, and pyrF using the cloned genes. Eur J Biochem 140:343–352. [PubMed][CrossRef]
397. Radzicka A, Wolfenden R. 1995. A proficient enzyme. Science 267:90–93. [PubMed][CrossRef]
398. Appleby TC, Kinsland C, Begley TP, Ealick SE. 2000. The crystal structure and mechanism of orotidine 5′-monophosphate decarboxylase. Proc Natl Acad Sci USA 97:2005–2010. [PubMed][CrossRef]
399. Harris P, Navarro Poulsen JC, Jensen KF, Larsen S. 2000. Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5′-monophosphate decarboxylase. Biochemistry 39:4217–4224. [PubMed][CrossRef]
400. Miller BG, Hassell AM, Wolfenden R, Milburn MV, Short SA. 2000. Anatomy of a proficient enzyme: the structure of orotidine 5′-monophosphate decarboxylase in the presence and absence of a potential transition state analog. Proc Natl Acad Sci USA 97:2011–2016. [PubMed][CrossRef]
401. Wu N, Mo Y, Gao J, Pai EF. 2000. Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase. Proc Natl Acad Sci USA 97:2017–2022. [PubMed][CrossRef]
402. Harris P, Poulsen JC, Jensen KF, Larsen S. 2002. Substrate binding induces domain movements in orotidine 5′-monophosphate decarboxylase. J Mol Biol 318:1019–1029. [PubMed][CrossRef]
403. Miller BG, Snider MJ, Short SA, Wolfenden R. 2000. Contribution of enzyme-phosphoribosyl contacts to catalysis by orotidine 5′-phosphate decarboxylase. Biochemistry 39:8113–8118. [PubMed][CrossRef]
404. Callahan BP, Miller BG. 2007. OMP decarboxylase—an enigma persists. Bioorg Chem 35:465–469. [PubMed][CrossRef]
405. Jensen KS, Johansson E, Jensen KF. 2007. Structural and enzymatic investigation of the Sulfolobus solfataricus uridylate kinase shows competitive UTP inhibition and the lack of GTP stimulation. Biochemistry 46:2745–2757. [PubMed][CrossRef]
406. Meier C, Carter LG, Manchini EJ, Owens RJ, Stuart DI, Esnouf RM. 3 July 2008. The crystal structure of UMP kinase from Bacillus antracis (BA 1797) reveals an allosteric nucleotide binding site. J Mol Biol [Epub ahead of print.]
407. Kelln RA. 1984. Evidence for involvement of pyrH + of an Escherichia coli K-12 F-prime factor in inhibiting construction of hybrid merodiploids with Salmonella typhimurium. Can J Microbiol 30:991–996.[PubMed]
408. Kholti A, Charlier D, Gigot D, Huysveld N, Roovers M, Glansdorff N. 1998. pyrH-encoded UMP-kinase directly participates in pyrimidine-specific modulation of promoter activity in Escherichia coli. J Mol Biol 280:571–582. [PubMed][CrossRef]
409. Lieberman I. 1956. Enzymatic amination of uridine triphosphate to cytidine triphosphate. J Biol Chem 222:765–775.[PubMed]
410. Weng M, Makaroff CA, Zalkin H. 1986. Nucleotide sequence of Escherichia coli pyrG encoding CTP synthetase. J Biol Chem 261:5568–5574.[PubMed]
411. Beck CF, Ingraham JL. 1971. Location on the chromosome of Salmonella typhimurium of genes governing pyrimidine metabolism. Mol Gen Genet 111:303–316. [PubMed][CrossRef]
412. Anderson PM. 1983. CTP synthetase from Escherichia coli: an improved purification procedure and characterization of hysteretic and enzyme concentration effects on kinetic properties. Biochemistry 22:3285–3292. [PubMed][CrossRef]
413. Robertson JG. 1995. Determination of subunit dissociation constants in native and inactivated CTP synthetase by sedimentation equilibrium. Biochemistry 34:7533–7541. [PubMed][CrossRef]
414. Levitzki A, Koshland DE, Jr. 1972. Ligand-induced dimer-to-tetramer transformation in cytosine triphosphate synthetase. Biochemistry 11:247–253. [PubMed][CrossRef]
415. Levitzki A, Koshland DE, Jr. 1972. Role of an allosteric effector. Guanosine triphosphate activation in cytosine triphosphate synthetase. Biochemistry 11:241–246. [PubMed][CrossRef]
416. Robertson JG, Villafranca JJ. 1993. Characterization of metal ion activation and inhibition of CTP synthetase. Biochemistry 32:3769–3777. [PubMed][CrossRef]
417. Wadskov-Hansen SL, Willemoës M, Martinussen J, Hammer K, Neuhard J, Larsen S. 2001. Cloning and verification of the Lactococcus lactis pyrG gene and characterization of the gene product, CTP synthase. J Biol Chem 276:38002–38009.[PubMed]
418. Willemoës M, Larsen S. 2003. Substrate inhibition of Lactococcus lactis cytidine 5′-triphosphate synthase by ammonium chloride is enhanced by salt-dependent tetramer dissociation. Arch Biochem Biophys 413:17–22. [PubMed][CrossRef]
419. Endrizzi JA, Kim H, Anderson PM, Baldwin EP. 2004. Crystal structure of Escherichia coli cytidine triphosphate synthetase, a nucleotide-regulated glutamine amidotransferase/ATP-dependent amidoligase fusion protein and homologue of anticancer and antiparasitic drug targets. Biochemistry 43:6447–6463. [PubMed][CrossRef]
420. Weng ML, Zalkin H. 1987. Structural role for a conserved region in the CTP synthetase glutamine amide transfer domain. J Bacteriol 169:3023–3028.[PubMed]
421. Bearne SL, Hekmat O, Macdonnell JE. 2001. Inhibition of Escherichia coli CTP synthase by glutamate gamma-semialdehyde and the role of the allosteric effector GTP in glutamine hydrolysis. Biochem J 356:223–232. [PubMed][CrossRef]
422. Levitzki A, Koshland DE Jr. 1971. Cytidine triphosphate synthetase. Covalent intermediates and mechanisms of action. Biochemistry 10:3365–3371. [PubMed][CrossRef]
423. Iyengar A, Bearne SL. 2003. Aspartate-107 and leucine-109 facilitate efficient coupling of glutamine hydrolysis to CTP synthesis by Escherichia coli CTP synthase. Biochem J 369:497–507. [PubMed][CrossRef]
424. Lunn FA, Bearne SL. 2004. Alternative substrates for wild-type and L109A E. coli CTP synthases: kinetic evidence for a constricted ammonia tunnel. Eur J Biochem 271:4204–4212. [PubMed][CrossRef]
425. Simard D, Hewitt KA, Lunn F, Iyengar A, Bearne SL. 2003. Limited proteolysis of Escherichia coli cytidine 5′-triphosphate synthase. Identification of residues required for CTP formation and GTP-dependent activation of glutamine hydrolysis. Eur J Biochem 270:2195–2206. [PubMed][CrossRef]
426. Lewis DA, Villafranca JJ. 1989. Investigation of the mechanism of CTP synthetase using rapid quench and isotope partitioning methods. Biochemistry 28:8454–8459. [PubMed][CrossRef]
427. von der Saal W, Anderson PM, Villafranca JJ. 1985. Mechanistic investigations of Escherichia coli cytidine-5′-triphosphate synthetase. Detection of an intermediate by positional isotope exchange experiments. J Biol Chem 260:14993–14997.[PubMed]
428. Long CW, Pardee AB. 1967. Cytidine triphosphate synthetase of Escherichia coli B. I. Purification and kinetics. J Biol Chem 242:4715–4721.[PubMed]
429. Lunn FA, Macdonnell JE, Bearne SL. 2008. Structural requirements for the activation of Escherichia coli CTP synthase by the allosteric effector GTP are stringent, but requirements for inhibition are lax. J Biol Chem 283:2010–2020. [PubMed][CrossRef]
430. MacDonnell JE, Lunn FA, Bearne SL. 2004. Inhibition of E. coli CTP synthase by the “positive” allosteric effector GTP. Biochim Biophys Acta 1699:213–220.[PubMed]
431. Willemoës M. 2004. Competition between ammonia derived from internal glutamine hydrolysis and hydroxylamine present in the solution for incorporation into UTP as catalysed by Lactococcus lactis CTP synthase. Arch Biochem Biophys 424:105–111. [PubMed][CrossRef]
432. Willemoës M. 2003. Thr-431 and Arg-433 are part of a conserved sequence motif of the glutamine amidotransferase domain of CTP synthases and are involved in GTP activation of the Lactococcus lactis enzyme. J Biol Chem 278:9407–9411. [PubMed][CrossRef]