Crystal structure of putative nucleotidyltransferase from H. pylori

Experimental Data Snapshot

  • Resolution: 2.17 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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Crystal structure of JHP933 from Helicobacter pylori J99 shows two-domain architecture with a DUF1814 family nucleotidyltransferase domain and a helical bundle domain.

Yoon, J.Y.Lee, S.J.Kim, D.J.Lee, B.J.Yang, J.K.Suh, S.W.

(2014) Proteins 82: 2275-2281

  • DOI: https://doi.org/10.1002/prot.24572
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The jhp0933 gene in the plasticity region of Helicobacter pylori J99 encodes a hypothetical protein (JHP933), which may play some roles in pathogenesis. Here, we have determined the crystal structure of JHP933 at 2.17 Å. It represents the first crystal structure of the DUF1814 protein family. JHP933 consists of two domains: an N-terminal domain of the nucleotidyltransferase (NTase) fold and a C-terminal helix bundle domain. A highly positively charged surface patch exists adjacent to the putative NTP binding site. Structural similarity of JHP933 to known NTases is very remote, suggesting that it may function as a novel NTase.

  • Organizational Affiliation

    Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 151-742, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
260Helicobacter pylori J99Mutation(s): 0 
Gene Names: jhp_0933
Find proteins for Q9ZKK2 (Helicobacter pylori (strain J99 / ATCC 700824))
Explore Q9ZKK2 
Go to UniProtKB:  Q9ZKK2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZKK2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.17 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.533α = 90
b = 82.533β = 90
c = 155.276γ = 120
Software Package:
Software NamePurpose
ADSCdata 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: 2014-04-09
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references