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Chapter 20 : The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase

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The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase, Page 1 of 2

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Abstract:

This chapter reviews the recognition specificity of a class II aminoacyl-tRNA synthetases (aaRS) and AspRS in detail. Class II aaRS are characterized by three signature motifs, each containing strictly conserved residues. The crystal structures of SerRS from and AspRS from yeast gave a clear structural explanation for the partition into the two classes. Indeed, class II aaRS contain a new fold, consisting of an antiparallel β sheet flanked by two α helices. The structures of the complex formed by tRNA and AspRS from yeast, with or without ATP correlate these motifs with their biological function; highly conserved residues from motifs 2 and 3 are responsible for ATP binding. Seven class II aaRS exhibit motifs 1 , 2 , and 3. More stringent sequence homology requirements led to the definition of subclasses. Class IIc aaRS (GlyRS, AlaRS, and PheRS) do not contain motif 1 and have a different quaternary organization. PheRS is an even more special case because it has the motif 2 and 3 characteristics of class II but behaves like a class I synthetase as to its primary site of aminoacylation.

Citation: Cavarelli J, Moras D. 1995. The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase, p 411-422. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch20

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Amino Acids
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Saccharomyces cerevisiae
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Aspartic Acid
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Escherichia coli
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Figures

Image of Figure 1.
Figure 1.

Alignment of aspartyl-tRNA synthetase sequences of different origins. The following abbreviations are used for mitochondria: Ysc, yeast cytoplasm; Hum, human; Rat, rat liver; See, ; Eco, ; Tth, ; Smt, mitochondria. Residues invariant in all synthetases are in boldface. The location of residues involved in tRNA and aspartic acid binding are shown above the sequence, and the location of residues involved in ATP binding as well as the three motifs of class II aaRS are shown below the sequence. The secondary structure elements for yeast AspRS are shown above the sequence with the same convention used in Fig. 2 (S, strand; H, helix).

Citation: Cavarelli J, Moras D. 1995. The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase, p 411-422. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch20
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Image of Figure 2.
Figure 2.

Yeast AspRS structure: overall structure (A), N-terminal domain (B), active site (C). Black and white figures were produced using the program Molscript, written by Kraulis ( ).

Citation: Cavarelli J, Moras D. 1995. The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase, p 411-422. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch20
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References

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1. Anselme, J., , and M. Hartlein .1989Asparaginyl-tRNA synthetase fromEscherichia coli has significant sequence homologies with yeast aspartyl-tRNA synthetase .Gene 84:481485.
2. Boeglin, M.,, J. C. Thierry,, and D. Moras. Submitted for publication.
3. Bossemeyer, D., , R. A. Engh,, V. Kinzel,, H. Ponstingl,, and R. Huber.1993 .Phosphotransferase and substrate binding mechanism of the cAMP-dependent protein kinase catalytic subunit from porcine heart as deduced from the 2.0 A structure of the complex with Mn2+ adenyl imidophosphate and inhibitor peptide PKI (5-24) .EMBO J 12:849859.
4. Brick, P.,, T. N. Bhat,, and D. M. Blow. 1989 .Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution. Interaction of the enzyme with tyrosyl adenylate intermediate. J. Mol. Biol.208:8398.
5. Brunie, S.,, C. Zelwer,, and J. L. Risler .1990 .Crystallographic study at 2.5 A resolution of the interaction of methionyl-tRNA synthetase formEscherichia coli with ATP.J. Mol. Biol. 216:411424.
6. Burbaum, J., , R. M. Starzyk,, and P. Schimmel .1990 .Understanding structural relationships in proteins of unsolved three-dimensional structure .Proteins 7:99111.
7. Carson, M.K. 1991 .Ribbvons 2.0. J. Appl.Crystallography 24:958961.
8. Cavarelli, J., , G. Eriani, , B. Rees, , M. Ruff, , M. Boegllin, , A. Mitschler,, F. Martin, , J. Gangloff, , J. C. Thierry, , and D. Moras .1994 .The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction. EMBO J. 13:327337.
9. Cavarelli, J., , and D. Moras .1993 .Recognition of tRNAs by aminoacyl-tRNA synthetases. FASEB J. 7:7986.
10. Cavarelli, J.,, B. Rees,, M. Ruff,, J. C. Thierry,, and D. Moras. 1993 .Yeast tRNAAsp recognition by its cognate class II aminoacyl-tRNA synthetase .Nature (London) 362:181184.
11. Cusack, S.,, C. Berthet-Colominas,, M. Härtlein,, N. Nassar, , and R. Leberman. 1990 .A second class of synthetase structure revealed by X-ray analysis ofEscherichia coli seryl-tRNA synthetase. Nature (London) 347:249255.
12. Cusack, S.,, M. Hartlein,, and R. Leberman. 1991 .Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases .Nucleic Acids Res .19:34893498.
13. Delarue, M.,, A. Poterszman,, S. Nikonov,, M. Garber,, D. Moras, , and J. C. Thierry .1994.EMBO J. 13:32193229.
14. Dietrich, A.,, R. Giege,, B. Cormarmond,, J. C. Thierry,, and D. Moras. 1990 .Crystallographic studies on the aspartyl-tRNA synthetase-tRNAAsp system from yeast .J. Mol. Biol. 138:129135.
15. Eiler, S.,, M. Boeglin, , F. Martin,, G. Eriani, , J. Gangloff,, J. C. Thierry,, and D. Moras .1992 .Crystallization of aspartyl-tRNA synthetase-tRNAAsp complex fromEscherichia coli and first crystallographic results J. Mol. Biol. 224:11711173.
16. Eriani, G.,, J. Cavarelli,, F. Martin,, G. Dirheimer,, D. Moras,, and J. Gangloff. 1993 .Functional interdependence of subunits and role of the class II invariant proline in yeast aspartyl-tRNA synthetase. Proc. Natl. Acad. Sci. USA 90:1081610820.
17. Eriani, G.,, M. Delarue,, O. Poch,, J. Gangloff,, and D. Moras. 1990 .Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature (London) 347:203206.
18. Eriani, G., , G. Prevost,, D. Kern, , P. Vincendon, , G. Dirheimer,, and J. Gangloff. 1991 .Cytoplasmic aspartyl-tRNA synthetase fromSaccharomyces cerevisiae. Study of its functional organisation by deletion analysis. Eur. J. Biochem .200:337343.
19. Fersht, A. R., , J. W. Knill-Jones, , H. Bedouelle,, and G. Winter. 1988 .Reconstruction by site-directed mutagenesis of the transition state for the activation of tyrosine by the tyrosyl-tRNA synthetase: a mobile loop envelopes the transition state in an induced-fit mechanism .Biochemistry 27:15811587.
20. Fraser, T. H., , and A. Rich .1975 .Amino acids are not all initially attached to the same position on transfer RNA molecules. Proc. Natl. Acad. Sci. USA 72:30443048.
21. Giege, R., , J. D. Puglisi, , and C. Florentz .1993 .tRNA structure and aminoacylation efficiency. Prog. Nucleic Acid Res. Mol. Biol. 45:129206.
22. Hecht, S. M. 1979. 2'-OH vs 3'-OHSpecificity in tRNA Aminoacylation. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y..
23. Hou, Y. M.,, and P. Schimmel .1988 .A simple structural feature is a major determinant of the identity of a transfer RNA .Nature (London) 333:140145.
24. Hountondji, C.,, P. Dessen,, and S. Blanquet.1986 .Sequence similarities among the family of aminoacyl-tRNA synthetases .Biochimie 68:10711078.
25. Hynes, T. R., , and R. O. Fox .1991 .The crystal structure of staphylococcal nuclease refined to 1.7 Å resolution .Proteins 10:92105.
26. Jakubowski, H. 1993. Proofreading and the evolution of a methyl donor function J. Biol. Chem. 268:65496553.
27. Janin, J., , S. Miller,, and C. Chothia .1988 .Surface, subunit interfaces and interior of oligomeric proteins. J. Mol. Biol .204:155164.
28. Jones, T. A., , J. Y. Zou, , S. W. Cowan, , and M. Kjeldgaard .1991 . Improved methods for building protein models in electron density maps and the location of errors in these models.Acta Crystallography A47:110119.
29. Kraulis, P. J. 1991 .Molscript: a program to produce both detailed and schematic plots of protein structures .J. Appl. Crystallography 24:946950.
30. Lapointe, J., , and R. Giege .1991. Transfer RNAs and aminoacyl-tRNA synthetases, p. 3569. In Translation in Eukaryotes. CRC Press, Inc., Boca Raton, Fla..
31. Leveque, F.,, P. Plateau, , P. Dessen, , and S. Blanquet .1990 .Homology of lysS and lysll, the twoEscherichia coli genes encoding distinct lysyl-tRNA synthetase species .Nucleic Acids Res .18:305312.
32. Lorber, B.,, D. Kern, , A. Dietrich,, J. Gangloff, , J. P. Ebel, , and R. Giege .1983 .Large scale purification and structural properties of yeast aspartyl-tRNA synthetase .Biochem. Biophys. Res. Commun. 117:259267.
33. McClain, W. H., , and K. Foss .1988 .Nucleotides that contribute to the identity ofEscherichia coli tRNAPhe. J. Mol.Biol .202:697709.
34. Mirande, M. 1991 .Aminoacyl-tRNA synthetase family from prokaryotes and eukaryotes: structural domains and their implications .Prog. Nucleic Acid Res. Mol. Biol .40:95142.
35. Moras, D. 1992 .Aminoacyl-tRNA synthetases .Curr. Opin. Struct. Biol .2:138142.
36. Moras, D.,, M. B. Comarmond,, J. Fischer,, R. Weiss,, J. C. Thierry. 1980 .Crystal structure of yeast tRNAAsp .Nature (London) 288:669674.
37. Muramatsu, T.,, K. Nishikawa,, F. Nemoto,, Y. Kuchino,, S. Nishimura,, T. Miyazawa,, and S. Yokoyama. 1988. Codon and ammo-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification .Nature (London) 336:179181.
38. Murzin, A. G. 1992. Familiar strangers.Nature (London) 360:635.
39. Murzin, A. G. 1993 .OB (oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J. 12:861867.
40. Musier-Forsyth, K.,, and P. Schimmel .1992 .Functional contacts of a transfer RNA synthetase with 2'-hydroxyl groups in the RNA minor groove. Nature (London) 357:513515.
41. Normanly, J.,, and J. Abelson .1989 .tRNA identity .Annu. Rev. Biochem .58:10291049.
42. Normanly, J.,, R. C. Ogden, , S. J. Horvath,, and J. Abelson .1986 .Changing the identity of a transfer RNA .Nature (London) 321:213219.
43. Normanly, J.,, T. Ollick, , and J. Abelson. 1992 .Eight base changes are sufficient to convert a leucine-inserting tRNA into a serine-inserting tRNA .Proc. Natl. Acad. Sci. USA 89:56805684.
44. Perret, V.,, A. Garcia,, H. Grosjean,, J. P. Ebel,, C. Florentz, , and R. Giege. 1990 .Relaxation of transfer RNA specificity by removal of modified nucleotides .Nature (London) 344:787789.
45. Podjarny, A.,, B. Rees, , J. C. Thierry,, J. Cavarelli, , J. C. Jesior,, M. Roth,, A. Lewitt-Bentley,, R. Kahn,, B. Lorber,, J. P. Ebel,, R. Giegé,, and D. Moras .1987. Yeast tRNAAsp-aspartyl-tRNA synthetase complex: low resolution crystal structure .J. Biomol. Struct. Dyn. 5:187198.
46. Poterszman, A.,, P. Plateau, , D. Moras,, S. Blanquet, M.-H. Mazauric,, and D. Kern .1993. Sequence, overproduction and crystallization of aspartyl-tRNA synthetase from Thermus thermophilus: implications for the structure of prokaryotic aspartyl-tRNA synthetases.FEBS Lett. 325(3):183186.
47. Puglisi, J. D.,, J. Putz, , C. Florentz, , and C. Giegé .1993 .Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase .Nucleic Acids Res .21:4149.
48. Putz, J.,, J. D. Puglisi,, C. Florentz,, and R. Giege. 1991 .Identity elements for specific aminoacylation of yeast tRNAAsp by cognate aspartyl-tRNA synthetase. Science 252:16961699.
49. Putz, J.,, J. D. Puglisi,, C. Florentz,, and R. Giege. 1993 .Additive, cooperative and anti-cooperative effects between identity nucleotides of a tRNA .EMBO J. 12:29492957.
50. Rossmann, M. G.,, D. Moras, , and K. W. Olsen. 1974 .Chemical and biological evolution of a nucleotide-binding protein. Nature (London) 250:194199.
51. Rould, M. A.,, J. J. Perona, , D. Söll,, and T. A. Steitz .1989 .Structure ofE. coli glutaminyl-tRNA synthetase complexed with tRNAGln and ATP at 2.8 Å resolution .Science 246:11351142.
52. Rould, M. A.,, J. J. Perona, , and T. A. Steitz .1991 .Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature (London) 352:213218.
53. Ruff, M.,, J. Caverelli,, V. Mikol,, B. Lorber,, A. Mitschler, , R. Giege,, J.-C. Thierry, , and D. Moras. 1988. A high resolution diffracting crystal form of the complex between yeast tRNAAsp and aspatyl-tRNA synthetase. J. Mol. Biol. 201:235236.
54. Ruff, M.,, S. Krishnaswamy,, M. Boeglin,, A. Poterszman,, A. Mitschler,, A. Podjarny,, B. Rees,, J.-C. Thierry, , and D. Moras. 1991. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNAAsp. Science 252:16821689.
55. Schimmel, P. 1987. Aminoacyl-tRNA synthetases: general scheme of structure-function relationships in the polypeptides and recognition of transfer RNAs. Annu. Rev. Biochem .56:125158.
56. Schimmel, P. 1989. Parameters for the molecular recognition of transfer RNAs .Biochemistry 28:27472759.
57. Schimmel, P.,, D. Söll,, and J. N. Abelson , (ed.).1979.Transfer RNA: Structure, Properties and Recognition. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y..
58. Schulman, L. H. 1991. Recognition oftRNAs by aminoacyl-tRNA synthetases .Prog. Nucleic Acid Res. Mol. Biol. 41:2387.
59. Shimizu, M.,, H. Asahara,, K. Tamura,, T. Hasegawa,, and H. Himeno. 1992 .The role of anticodon bases and the discriminator nucleotide in the recognition of someE. coli tRNA by their aminoacyl-tRNA synthetases. J. Mol. Evol. 35:436443.
60. Sixma, K.,, S. E. Pronk,, K. H. Kalk,, B. van Zanten, , A. M. Berghuis,,and W. G. J. Hol. 1992.Lactose binding to heat-labile enterotoxin revealed by X-ray crystallography. Nature (London) 355:561564.
61. Söll, D. 1991. The accuracy of aminoacylation—ensuring the fidelity of the genetic code .Experientia 46:10891096.
62. Sprinzl, M., , and M. Cramer .1975 .Site of aminoacylation of tRNAs fromEscherichia coli with respect to the 2'- or 3'-hydroxyl group of the terminal adenosine.Proc. Natl. Acad. Sci. USA 72:30493053.
63. Stein, P. E.,, A. Boodhoo, , G. J. Tyrrell,, J. L. Brunton, , and R. J. Read .1992 .Crystal structure of cell-binding B oligomer of verotoxin-1 fromE. coli .Nature (London) 355:748750.
64. Swaminathan, S.,, W. Furey, , J. Pletcher,, and M. Sax .1992 .Crystal structure of staphylococcal enterotoxin B, a superantigen .Nature (London) 359:801806.
65. Tzagoloff, A., , D. Gatti, , and A. Gampel .1990 .Mitochondrial aminoacyl-tRNA synthetases .Prog. Nucleic Acid Res. Mol. Biol. 39:129158.
66. Westhof, E.,, P. Dumas, , and D. Moras. 1985 .Crystallographic refinement of yeast aspartic acid transfer RNA .J. Mol. Biol. 184:119145.
67. Westhof, E.,, P. Dumas,, and D. Moras. 1988. Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals. Acta Crystallography A44:112123.

Tables

Generic image for table
Table 1.

Classification of aminoacyl-tRNA synthetases

Aminoacyl tRNA synthetases charge their amino acid to the 2′-OH (class I) or the 3′-OH (class II) of the ribose of the terminal adenosine. The ATP binding site is different for the two classes.

The aaRS does not recognize the anticodon.

The aaRS structure has been determined in at least one species.

The aaRS needs the tRNA for aminoacyladenylate formation.

Motifs 2 and 3 only.

Citation: Cavarelli J, Moras D. 1995. The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase, p 411-422. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch20
Generic image for table
Table 2.

Homology and identity in AspRS

Ysc, yeast cytoplasmic; Hum, human; Rat, rat liver; See; Eco, ; Tth, ; Smt, mitochondrial.

Citation: Cavarelli J, Moras D. 1995. The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase, p 411-422. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch20
Generic image for table
Table 3.

Crystallographic data for the AspRS system

The solvent content values given here assume an average density of the crystals of 1.15 g/cm. The molecular masses used are as follows: yeast AspRS (62.5 kDa per monomer, 557 residues); AspRS (66 kDa per monomer, 591 residues); AspRS (66 kDa per monomer, 580 residues); yeast tRNA (24,160 Da, 75 nucleotides); tRNA (25,000 Da, 77 nucleotides).

Citation: Cavarelli J, Moras D. 1995. The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase, p 411-422. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch20

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