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

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 

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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: https://doi.org/10.1093/nar/gkr1305
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin G-binding protein G, Virulence-associated protein D
A, B
160Streptococcus 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsO05728P19909
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • 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
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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