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EcoSal Plus

Domain 4:

Synthesis and Processing of Macromolecules

The DNA Exonucleases of

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  • Author: Susan T. Lovett1
  • Editor: Susan T. Lovett2
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Biology and Rosenstiel Basic Medical Sciences Research Center, MS029, Brandeis University, Waltham, MA 02454-9110; 2: Brandeis University, Waltham, MA
  • Received 05 May 2010 Accepted 21 July 2010 Published 09 June 2011
  • Address correspondence to Susan T. Lovett lovett@brandeis.edu.
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  • Abstract:

    DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry, and biological functions of the 17 exonucleases currently identified in the bacterium . These include the exonucleases associated with DNA polymerases I (), II (), and III (); Exonucleases I (), III (), IV, VII (), IX (), and X (); the RecBCD, RecJ, and RecE exonucleases; SbcCD endo/exonucleases; the DNA exonuclease activities of RNase T () and Endonuclease IV (); and TatD. These enzymes are diverse in terms of substrate specificity and biochemical properties and have specialized biological roles. Most of these enzymes fall into structural families with characteristic sequence motifs, and members of many of these families can be found in all domains of life.

  • Citation: Lovett S. 2011. The DNA Exonucleases of , EcoSal Plus 2011; doi:10.1128/ecosalplus.4.4.7

Key Concept Ranking

DNA Repair Enzyme
0.6670078
DNA Polymerase I
0.54377455
DNA Polymerase III
0.5093979
0.6670078

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ecosalplus.4.4.7.citations
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/content/journal/ecosalplus/10.1128/ecosalplus.4.4.7
2011-06-09
2017-07-21

Abstract:

DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry, and biological functions of the 17 exonucleases currently identified in the bacterium . These include the exonucleases associated with DNA polymerases I (), II (), and III (); Exonucleases I (), III (), IV, VII (), IX (), and X (); the RecBCD, RecJ, and RecE exonucleases; SbcCD endo/exonucleases; the DNA exonuclease activities of RNase T () and Endonuclease IV (); and TatD. These enzymes are diverse in terms of substrate specificity and biochemical properties and have specialized biological roles. Most of these enzymes fall into structural families with characteristic sequence motifs, and members of many of these families can be found in all domains of life.

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Figures

Image of Figure 1
Figure 1

Shown are aligned amino acid sequences of Exonuclease I (ExoI), Exonuclease X (ExoX), oligoribonuclease (ORN), RNase D, RNase T, and the 3′ exonucleases of DNA polymerases I, II, and III. Conserved acid residues are shown in bold and comprise metal coordination residues for those proteins with determined three-dimensional structure. Numbers refer to amino acid residues not shown. (B) Structure of three members of the DnaQ/DEDD superfamily: DnaQ, ExoI, and polymerase I 3′ exonuclease domain. This figure is republished with permission from Hamdan et al. 2002 ( 2 ).

Citation: Lovett S. 2011. The DNA Exonucleases of , EcoSal Plus 2011; doi:10.1128/ecosalplus.4.4.7
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Image of Figure 2
Figure 2

Image from RCSB PDB (www.pdb.org), PDB ID: 1TAQ ( 1995. Crystal structure of DNA polymerase. 612–616). (B) Okazaki maturation by polymerase I. Polymerization at a gap causes displacement of lagging strand RNA primer (orange), which is cleaved by 5′ flap endonuclease activity.

Citation: Lovett S. 2011. The DNA Exonucleases of , EcoSal Plus 2011; doi:10.1128/ecosalplus.4.4.7
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Image of Figure 3
Figure 3

(Images from RCSB PDB [www.pdb.org] ID: 2ZXP, 2010. Structure of RecJ exonuclease defines its specificity for single-stranded DNA. 9762–9769, and PDB ID: 1FXX, 2000. Structure of exonuclease I suggests how processivity is achieved. 1125–1128). RecJ digests ssDNA 5′ to 3′ and ExoI digests it 3′ to 5′. Both produce mononucleotide products.

Citation: Lovett S. 2011. The DNA Exonucleases of , EcoSal Plus 2011; doi:10.1128/ecosalplus.4.4.7
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Figure 4

(www.pdb.org)] (PDB ID: 1AKO, (B) Structure of Endonuclease IV, showing 3 Zn ions (PDB ID: 1QTW, 1999. Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. 397–408). (C) Activities of ExoIII and Endonuclease IV: 3′ phosphatase, 3′ to 5′ exonuclease, AP (abasic) endonuclease.

Citation: Lovett S. 2011. The DNA Exonucleases of , EcoSal Plus 2011; doi:10.1128/ecosalplus.4.4.7
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Figure 5

(B) Activities of the enzyme, before and after Chi recognition. Figure reproduced with permission from Dillingham and Kowalczykowski 2008 ( 145 ).

Citation: Lovett S. 2011. The DNA Exonucleases of , EcoSal Plus 2011; doi:10.1128/ecosalplus.4.4.7
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Figure 6

(Image from RCSB PDB [www.pdb.org] PDB ID: 3H4R, 2009. Crystal structure of RecE protein reveals a toroidal tetramer for processing double-stranded DNA breaks. 690–702). (B) Alignment of active site regions of RecE and RecB nucleases. (C) 5′ to 3′ exonuclease activity of RecE on dsDNA.

Citation: Lovett S. 2011. The DNA Exonucleases of , EcoSal Plus 2011; doi:10.1128/ecosalplus.4.4.7
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Tables

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Table 1.

DNA exonucleases of

Citation: Lovett S. 2011. The DNA Exonucleases of , EcoSal Plus 2011; doi:10.1128/ecosalplus.4.4.7

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