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 1.1 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: 10.1016/j.cell.2011.03.005
  • Primary Citation of Related Structures:  

  • 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 G ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exonuclease 1
Y, Z
352Homo sapiensMutation(s): 1 
Gene Names: EXO1 (EXOI, HEX1)
EC: 3.1.-.-
Find proteins for Q9UQ84 (Homo sapiens)
Go to Gene View: EXO1
Go to UniProtKB:  Q9UQ84
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3')C,A13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')D,B10N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
Y, Z
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
Y, Z
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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 = 90.00
b = 95.467β = 90.00
c = 99.777γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SHARPphasing
HKL-2000data reduction
HKL-2000data collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance