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- PDB-8txr: E. coli ExoVII(H238A) -

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Basic information

Entry
Database: PDB / ID: 8txr
TitleE. coli ExoVII(H238A)
Components
  • Exodeoxyribonuclease 7 large subunit
  • Exodeoxyribonuclease 7 small subunit
KeywordsDNA BINDING PROTEIN / Exonuclease / Endonuclease / DNA repair
Function / homology
Function and homology information


exodeoxyribonuclease VII / exodeoxyribonuclease VII activity / exodeoxyribonuclease VII complex / DNA catabolic process / mismatch repair / DNA binding / cytosol / cytoplasm
Similarity search - Function
Exonuclease VII, large subunit / Exonuclease VII, large subunit, C-terminal / OB-fold nucleic acid binding domain / Exonuclease VII, large subunit / OB-fold nucleic acid binding domain / Exonuclease VII, small subunit / Exonuclease VII, small subunit superfamily / Exonuclease VII small subunit
Similarity search - Domain/homology
Exodeoxyribonuclease 7 large subunit / Exodeoxyribonuclease 7 small subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLiu, C. / Berger, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA263778 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structure of exonuclease VII.
Authors: Chuan Liu / Glenn Hauk / Qianyun Yan / James M Berger /
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.
History
DepositionAug 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / em_author_list
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_author_list.author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exodeoxyribonuclease 7 large subunit
C: Exodeoxyribonuclease 7 large subunit
i: Exodeoxyribonuclease 7 small subunit
c: Exodeoxyribonuclease 7 small subunit
g: Exodeoxyribonuclease 7 small subunit
h: Exodeoxyribonuclease 7 small subunit
a: Exodeoxyribonuclease 7 small subunit
b: Exodeoxyribonuclease 7 small subunit
B: Exodeoxyribonuclease 7 large subunit
o: Exodeoxyribonuclease 7 small subunit
p: Exodeoxyribonuclease 7 small subunit
D: Exodeoxyribonuclease 7 large subunit
m: Exodeoxyribonuclease 7 small subunit
n: Exodeoxyribonuclease 7 small subunit
j: Exodeoxyribonuclease 7 small subunit
k: Exodeoxyribonuclease 7 small subunit
l: Exodeoxyribonuclease 7 small subunit
d: Exodeoxyribonuclease 7 small subunit
e: Exodeoxyribonuclease 7 small subunit
f: Exodeoxyribonuclease 7 small subunit


Theoretical massNumber of molelcules
Total (without water)350,71920
Polymers350,71920
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Exodeoxyribonuclease 7 large subunit /


Mass: 51840.141 Da / Num. of mol.: 4 / Mutation: H238A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: xseA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P04994
#2: Protein
Exodeoxyribonuclease 7 small subunit /


Mass: 8959.877 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: xseB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0A8G9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: XseA4-XseB24 complex of ExoVII / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.42 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1750 nm / Nominal defocus min: 750 nm
Image recordingElectron dose: 50.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 497337 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319266
ELECTRON MICROSCOPYf_angle_d0.4425997
ELECTRON MICROSCOPYf_dihedral_angle_d11.5427447
ELECTRON MICROSCOPYf_chiral_restr0.0362942
ELECTRON MICROSCOPYf_plane_restr0.0033479

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