3QE9

Crystal structure of human exonuclease 1 Exo1 (D173A) in complex with DNA (complex I)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family.

Orans, J.McSweeney, E.A.Iyer, R.R.Hast, M.A.Hellinga, H.W.Modrich, P.Beese, L.S.

(2011) Cell 145: 212-223

  • DOI: https://doi.org/10.1016/j.cell.2011.03.005
  • Primary Citation of Related Structures:  
    3QE9, 3QEA, 3QEB

  • PubMed Abstract: 

    Human exonuclease 1 (hExo1) plays important roles in DNA repair and recombination processes that maintain genomic integrity. It is a member of the 5' structure-specific nuclease family of exonucleases and endonucleases that includes FEN-1, XPG, and GEN1. We present structures of hExo1 in complex with a DNA substrate, followed by mutagenesis studies, and propose a common mechanism by which this nuclease family recognizes and processes diverse DNA structures. hExo1 induces a sharp bend in the DNA at nicks or gaps. Frayed 5' ends of nicked duplexes resemble flap junctions, unifying the mechanisms of endo- and exonucleolytic processing. Conformational control of a mobile region in the catalytic site suggests a mechanism for allosteric regulation by binding to protein partners. The relative arrangement of substrate binding sites in these enzymes provides an elegant solution to a complex geometrical puzzle of substrate recognition and processing.


  • Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exonuclease 1A [auth Y],
D [auth Z]
352Homo sapiensMutation(s): 1 
Gene Names: EXO1EXOIHEX1
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQ84 (Homo sapiens)
Explore Q9UQ84 
Go to UniProtKB:  Q9UQ84
PHAROS:  Q9UQ84
GTEx:  ENSG00000174371 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQ84
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3')B [auth C],
E [auth A]
13N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')C [auth D],
F [auth B]
10N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.504α = 90
b = 95.467β = 90
c = 99.777γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations