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-Structure paper
Title | Structure of exonuclease VII. |
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Journal, issue, pages | Proc Natl Acad Sci U S A, Vol. 121, Issue 5, Page e2319644121, Year 2024 |
Publish date | Jan 30, 2024 |
Authors | Chuan Liu / Glenn Hauk / Qianyun Yan / James M Berger / |
PubMed Abstract | Exonuclease VII (ExoVII) is a ubiquitous bacterial nuclease. Encoded by the and genes, ExoVII participates in multiple nucleic acid-dependent pathways including the processing of multicopy single- ...Exonuclease VII (ExoVII) is a ubiquitous bacterial nuclease. Encoded by the and genes, ExoVII participates in multiple nucleic acid-dependent pathways including the processing of multicopy single-stranded DNA and the repair of covalent DNA-protein crosslinks (DPCs). Although many biochemical properties of ExoVII have been defined, little is known about its structure/function relationships. Here, we use cryoelectron microscopy (cryoEM) to determine that ExoVII comprises a highly elongated XseA·XseB holo-complex. Each XseA subunit dimerizes through a central extended α-helical segment decorated by six XseB subunits and a C-terminal, domain-swapped β-barrel element; two XseA·XseB subcomplexes further associate using N-terminal OB (oligonucleotide/oligosaccharide-binding) folds and catalytic domains to form a spindle-shaped, catenated octaicosamer. The catalytic domains of XseA, which adopt a nuclease fold related to 3-dehydroquinate dehydratases, are sequestered in the center of the complex and accessible only through large pores formed between XseA tetramers. The architectural organization of ExoVII, combined with biochemical studies, indicate that substrate selectivity is controlled by steric access to its nuclease elements and that tetramer dissociation results from substrate DNA binding. Despite a lack of sequence and fold homology, the physical organization of ExoVII is reminiscent of Mre11·Rad50/SbcCD ATP (adenosine triphosphate)-dependent nucleases used in the repair of double-stranded DNA breaks, including those formed by DPCs through aberrant topoisomerase activity, suggesting that there may have been convergent evolutionary pressure to contend with such damage events. |
External links | Proc Natl Acad Sci U S A / PubMed:38271335 / PubMed Central |
Methods | EM (single particle) |
Resolution | 3.6 - 6.4 Å |
Structure data | EMDB-41699: The consensus map of E. coli ExoVII(H238A) EMDB-41700: Head map of E. coli ExoVII (H238A) EMDB-41701: The tail map of E. coli ExoVII(H238A) EMDB-41702: The half complex of E. coli ExoVII(H238A) EMDB-41704, PDB-8txr: |
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Keywords | DNA BINDING PROTEIN / Exonuclease / Endonuclease / DNA repair |