1ODG | pdb_00001odg

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

• PDB DOI: https://doi.org/10.2210/pdb1ODG/pdb
• NAKB: 1ODG

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-02-19 Released: 2003-03-13 
• Deposition Author(s): Bunting, K.A., Roe, S.M., Headley, A., Brown, T., Savva, R., Pearl, L.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.356 (Depositor), 0.356 (DCC) 
• R-Value Work: 
  0.287 (Depositor), 0.290 (DCC) 
• R-Value Observed: 
  0.287 (Depositor) 

Starting Model: experimental

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: 12626704 
• DOI: https://doi.org/10.1093/nar/gkg273
• Primary Citation Related Structures: 
  1ODG


• 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 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 23.02 kDa 
• Atom Count: 1,672 
• Modeled Residue Count: 158 
• Deposited Residue Count: 158 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA MISMATCH ENDONUCLEASE	A	134	Escherichia coli	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for P09184 (Escherichia coli (strain K12)) Explore P09184  Go to UniProtKB:  P09184

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*AP*GP*GP*CP*5CM*TP*GP*GP*AP*TP*CP)-3'	B [auth F], C [auth W]	12	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.356 (Depositor), 0.356 (DCC) 
• R-Value Work:  0.287 (Depositor), 0.290 (DCC) 
• R-Value Observed: 0.287 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.805	α = 90
b = 102.805	β = 90
c = 64.29	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-13 
Deposition Author(s): Bunting, K.A., Roe, S.M., Headley, A., Brown, T., Savva, R., Pearl, L.H.

Revision History  

• Version 1.0: 2003-03-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description