5H0M

Crystal structure of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease with zinc ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


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Literature

Structural and functional characterization of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease

Zhang, L.K.Xu, D.D.Huang, Y.C.Zhu, X.Y.Rui, M.W.Wan, T.Zheng, X.Shen, Y.L.Chen, X.D.Ma, K.S.Gong, Y.

(2017) Sci Rep 7: 42542-42542

  • DOI: 10.1038/srep42542
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HNH endonucleases in bacteriophages play a variety of roles in the phage lifecycle as key components of phage DNA packaging machines. The deep-sea thermophilic bacteriophage Geobacillus virus E2 (GVE2) encodes an HNH endonuclease (GVE2 HNHE). Here, t ...

    HNH endonucleases in bacteriophages play a variety of roles in the phage lifecycle as key components of phage DNA packaging machines. The deep-sea thermophilic bacteriophage Geobacillus virus E2 (GVE2) encodes an HNH endonuclease (GVE2 HNHE). Here, the crystal structure of GVE2 HNHE is reported. This is the first structural study of a thermostable HNH endonuclease from a thermophilic bacteriophage. Structural comparison reveals that GVE2 HNHE possesses a typical ββα-metal fold and Zn-finger motif similar to those of HNH endonucleases from other bacteriophages, apart from containing an extra α-helix, suggesting conservation of these enzymes among bacteriophages. Biochemical analysis suggests that the alanine substitutions of the conserved residues (H93, N109 and H118) in the HNH motif of GVE2 HNHE abolished 94%, 60% and 83% of nicking activity, respectively. Compared to the wild type enzyme, the H93A mutant displayed almost the same conformation while the N108A and H118A mutants had different conformations. In addition, the wild type enzyme was more thermostable than the mutants. In the presence of Mn 2+ or Zn 2+ , the wild type enzyme displayed distinct DNA nicking patterns. However, high Mn 2+ concentrations were needed for the N109A and H118A mutants to nick DNA while Zn 2+ inactivated their nicking activity.


    Organizational Affiliation

    State Key Laboratory of Microbial Technology, Shandong University, China.,Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, China.,Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China.,State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Marine Science &Technology Institute Department of Environmental Science and Engineering, Yangzhou University, China.,Department of Biology, University of Waterloo, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HNH endonuclease
A
130Geobacillus virus E2Mutation(s): 0 
Find proteins for A0A1U7Q1S7 (Geobacillus virus E2)
Go to UniProtKB:  A0A1U7Q1S7
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.144 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 66.264α = 90.00
b = 66.264β = 90.00
c = 51.484γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China--

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release