7LW8

Human Exonuclease 5 crystal structure in complex with a ssDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart.

Hambarde, S.Tsai, C.L.Pandita, R.K.Bacolla, A.Maitra, A.Charaka, V.Hunt, C.R.Kumar, R.Limbo, O.Le Meur, R.Chazin, W.J.Tsutakawa, S.E.Russell, P.Schlacher, K.Pandita, T.K.Tainer, J.A.

(2021) Mol Cell 81: 2989

  • DOI: https://doi.org/10.1016/j.molcel.2021.05.027
  • Primary Citation of Related Structures:  
    7LW7, 7LW8, 7LW9, 7LWA

  • PubMed Abstract: 

    Stalled DNA replication fork restart after stress as orchestrated by ATR kinase, BLM helicase, and structure-specific nucleases enables replication, cell survival, and genome stability. Here we unveil human exonuclease V (EXO5) as an ATR-regulated DNA structure-specific nuclease and BLM partner for replication fork restart. We find that elevated EXO5 in tumors correlates with increased mutation loads and poor patient survival, suggesting that EXO5 upregulation has oncogenic potential. Structural, mechanistic, and mutational analyses of EXO5 and EXO5-DNA complexes reveal a single-stranded DNA binding channel with an adjacent ATR phosphorylation motif (T88Q89) that regulates EXO5 nuclease activity and BLM binding identified by mass spectrometric analysis. EXO5 phospho-mimetic mutant rescues the restart defect from EXO5 depletion that decreases fork progression, DNA damage repair, and cell survival. EXO5 depletion furthermore rescues survival of FANCA-deficient cells and indicates EXO5 functions epistatically with SMARCAL1 and BLM. Thus, an EXO5 axis connects ATR and BLM in directing replication fork restart.


  • Organizational Affiliation

    Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Neurosurgery, The Houston Methodist Research Institute, Houston, TX 77030, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exonuclease V346Homo sapiensMutation(s): 1 
Gene Names: EXO5C1orf176DEM1
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H790 (Homo sapiens)
Explore Q9H790 
Go to UniProtKB:  Q9H790
PHAROS:  Q9H790
GTEx:  ENSG00000164002 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H790
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')12synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.17α = 90
b = 83.98β = 90
c = 96.355γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR35CA22043
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01 CA092584

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description