4XPU

The crystal structure of EndoV from E.coli

  • Classification: HYDROLASE
  • Organism(s): Escherichia coli S88
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-01-18 Released: 2015-08-19 
  • Deposition Author(s): Xie, W., Zhang, Z.
  • Funding Organization(s): National Sciences Foundation of China, Guangdong Innovative Research Team Program

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of E. coli endonuclease V, an essential enzyme for deamination repair

Zhang, Z.Jia, Q.Zhou, C.Xie, W.

(2015) Sci Rep 5: 12754-12754

  • DOI: 10.1038/srep12754
  • Primary Citation of Related Structures:  
    4XPU

  • PubMed Abstract: 
  • Endonuclease V (EndoV) is a ubiquitous protein present in all three kingdoms of life, responsible for the specific cleavages at the second phosphodiester bond 3' to inosine. E. coli EndoV (EcEndoV) is the first member discovered in the EndoV family. ...

    Endonuclease V (EndoV) is a ubiquitous protein present in all three kingdoms of life, responsible for the specific cleavages at the second phosphodiester bond 3' to inosine. E. coli EndoV (EcEndoV) is the first member discovered in the EndoV family. It is a small protein with a compact gene organization, yet with a wide spectrum of substrate specificities. However, the structural basis of its substrate recognition is not well understood. In this study, we determined the 2.4 Å crystal structure of EcEndoV. The enzyme preserves the general 'RNase H-like motif' structure. Two subunits are almost fully resolved in the asymmetric unit, but they are not related by any 2-fold axes. Rather, they establish "head-to-shoulder" contacts with loose interactions between each other. Mutational studies show that mutations that disrupt the association mode of the two subunits also decrease the cleavage efficiencies of the enzyme. Further biochemical studies suggest that EcEndoV is able to bind to single-stranded, undamaged DNA substrates without sequence specificity, and forms two types of complexes in a metal-independent manner, which may explain the wide spectrum of substrate specificities of EcEndoV.


    Organizational Affiliation

    1] State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou 510275, People's Republic of China [2] Center for Cellular &Structural biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou 510006, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endonuclease VAB217Escherichia coli S88Mutation(s): 0 
Gene Names: nfiECS88_4459
EC: 3.1.21.7
Find proteins for B7MIY4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Explore B7MIY4 
Go to UniProtKB:  B7MIY4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.892α = 90
b = 84.783β = 90
c = 91.507γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-01-18 
  • Released Date: 2015-08-19 
  • Deposition Author(s): Xie, W., Zhang, Z.

Funding OrganizationLocationGrant Number
National Sciences Foundation of ChinaChina31100579
Guangdong Innovative Research Team ProgramChina2011Y038

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Data collection