1ODG

Very-short-patch DNA repair endonuclease bound to its reaction product site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.287 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Escherichia Coli Dcm Very-Short-Patch DNA Repair Endonuclease Bound to its Reaction Product-Site in a DNA Superhelix

Bunting, K.A.Roe, S.M.Headley, A.Brown, T.Savva, R.Pearl, L.H.

(2003) Nucleic Acids Res. 31: 1633


  • PubMed Abstract: 
  • Very-short-patch repair (Vsr) enzymes occur in a variety of bacteria, where they initiate nucleotide excision repair of G:T mismatches arising by deamination of 5-methyl-cytosines in specific regulatory sequences. We have now determined the structure ...

    Very-short-patch repair (Vsr) enzymes occur in a variety of bacteria, where they initiate nucleotide excision repair of G:T mismatches arising by deamination of 5-methyl-cytosines in specific regulatory sequences. We have now determined the structure of the archetypal dcm-Vsr endonuclease from Escherichia coli bound to the cleaved authentic hemi-deaminated/hemi-methylated dcm sequence 5'-C-OH-3' 5'-p-T-p-A-p-G-p-G-3'/3'-G-p-G-p-T-p(Me5)C-p-C formed by self-assembly of a 12mer oligonucleotide into a continuous nicked DNA superhelix. The structure reveals the presence of a Hoogsteen base pair within the deaminated recognition sequence and the substantial distortions of the DNA that accompany Vsr binding to product sites.


    Organizational Affiliation

    Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA MISMATCH ENDONUCLEASE
A
134Escherichia coli (strain K12)Gene Names: vsr
EC: 3.1.-.-
Find proteins for P09184 (Escherichia coli (strain K12))
Go to UniProtKB:  P09184
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*AP*GP*GP*CP*5CM*TP*GP*GP*AP*TP*CP)-3'F,W12Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
F, W
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.287 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 102.805α = 90.00
b = 102.805β = 90.00
c = 64.290γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALAdata scaling
AMoREphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance