1VSR | pdb_00001vsr

VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE FROM ESCHERICHIA COLI

• PDB DOI: https://doi.org/10.2210/pdb1VSR/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1999-02-13 Released: 1999-10-27 
• Deposition Author(s): Tsutakawa, S.E., Muto, T., Jingami, H., Kunishima, N., Ariyoshi, M., Kohda, D., Nakagawa, M., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.193 (DCC) 

Literature

Crystallographic and functional studies of very short patch repair endonuclease.

Tsutakawa, S.E., Muto, T., Kawate, T., Jingami, H., Kunishima, N., Ariyoshi, M., Kohda, D., Nakagawa, M., Morikawa, K.

(1999) Mol Cell 3: 621-628

• PubMed: 10360178 
• DOI: https://doi.org/10.1016/s1097-2765(00)80355-x
• Primary Citation Related Structures: 
  1VSR


• PubMed Abstract: 
  

  Vsr endonuclease plays a crucial role in the repair of TG mismatched base pairs, which are generated by the spontaneous degradation of methylated cytidines; Vsr recognizes the mismatched base pair and cleaves the phosphate backbone 5' to the thymidine. We have determined the crystal structure of a truncated form of this endonuclease at 1.8 A resolution. The protein contains one structural zinc-binding module. Unexpectedly, its overall topology resembles members of the type II restriction endonuclease family. Subsequent mutational and biochemical analyses showed that certain elements in the catalytic site are also conserved. However, the identification of a critical histidine and evidence of an active site metal-binding coordination that is novel to endonucleases indicate a distinct catalytic mechanism.

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Organizational Affiliation: 
• Department of Structural Biology, Biomolecular Engineering Research Institute (BERI), Osaka, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.85 kDa 
• Atom Count: 1,161 
• Modeled Residue Count: 134 
• Deposited Residue Count: 136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (VSR ENDONUCLEASE)	A	136	Escherichia coli K-12	Mutation(s): 0  Gene Names: VSR EC: 3.1
UniProt
Find proteins for P09184 (Escherichia coli (strain K12)) Explore P09184  Go to UniProtKB:  P09184

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.193 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.02	α = 90
b = 54.24	β = 90
c = 73.52	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-10-27 
Deposition Author(s): Tsutakawa, S.E., Muto, T., Jingami, H., Kunishima, N., Ariyoshi, M., Kohda, D., Nakagawa, M., Morikawa, K.

Revision History  

• Version 1.0: 1999-10-27
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations