3UI3

Structural and Biochemical Characterization of HP0315 from Helicobacter pylori as a VapD Protein with an Endoribonuclease Activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and biochemical characterization of HP0315 from Helicobacter pylori as a VapD protein with an endoribonuclease activity.

Kwon, A.R.Kim, J.H.Park, S.J.Lee, K.Y.Min, Y.H.Im, H.Lee, I.Lee, K.Y.Lee, B.J.

(2012) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkr1305
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • VapD-like virulence-associated proteins have been found in many organisms, but little is known about this protein family including the 3D structure of these proteins. Recently, a relationship between the Cas2 family of ribonucleases associated with t ...

    VapD-like virulence-associated proteins have been found in many organisms, but little is known about this protein family including the 3D structure of these proteins. Recently, a relationship between the Cas2 family of ribonucleases associated with the CRISPR system of microbial immunity and VapD was suggested. Here, we show for the first time the structure of a member of the VapD family and present a relationship of VapD with Cas2 family and toxin-antitoxin (TA) systems. The crystal structure of HP0315 from Helicobacter pylori was solved at a resolution of 2.8 Å. The structure of HP0315, which has a modified ferredoxin-like fold, is very similar to that of the Cas2 family. Like Cas2 proteins, HP0315 shows endoribonuclease activity. HP0315-cleaved mRNA, mainly before A and G nucleotides preferentially, which means that HP0315 has purine-specific endoribonuclease activity. Mutagenesis studies of HP0315 revealed that D7, L13, S43 and D76 residues are important for RNase activity, in contrast, to the Cas2 family. HP0315 is arranged as an operon with HP0316, which was found to be an antitoxin-related protein. However, HP0315 is not a component of the TA system. Thus, HP0315 may be an evolutionary intermediate which does not belong to either the Cas2 family or TA system.


    Organizational Affiliation

    Department of Herbal Skin Care, College of Herbal Bio-Industry, Daegu Haany University, Gyeongsan 712-715, Korea.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin G-binding protein G, Virulence-associated protein DA, B160Streptococcus sp. 'group GHelicobacter pylori 26695
This entity is chimeric
Mutation(s): 0 
Gene Names: HP_0315spgvapD
EC: 3.1
Find proteins for O05728 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O05728 
Go to UniProtKB:  O05728
Find proteins for P19909 (Streptococcus sp. group G)
Explore P19909 
Go to UniProtKB:  P19909
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.81α = 90
b = 77.81β = 90
c = 106.31γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SnBphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Refinement description, Source and taxonomy