3LWG | pdb_00003lwg

Crystal structure of HP0420-homologue C46A from helicobacter felis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.185 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Crystal structure and functional insight of HP0420-homolog from Helicobacter felis

Piao, S.Jin, X.L.Yun, B.-Y.Kim, N.Cho, H.-S.Fukuda, M.Lee, H.Ha, N.-C.

(2010) Biochem Biophys Res Commun 394: 940-946

  • DOI: https://doi.org/10.1016/j.bbrc.2010.03.087
  • Primary Citation Related Structures: 
    3LW3, 3LWG

  • PubMed Abstract: 

    Helicobacter pylori infect more than half of the world's population and are considered a cause of peptic ulcer disease and gastric cancer. Recently, hypothetical gene HP0421 was identified in H. pylori as a cholesterol alpha-glucosyltransferase, which is required to synthesize cholesteryl glucosides, essential cell wall components of the bacteria. In the same gene-cluster, HP0420 was co-identified, whose function remains unknown. Here we report the crystal structure of HP0420-homolog of H. felis (HF0420) to gain insight into the function of HP0420. The crystal structure, combined with size-exclusion chromatography, reveals that HF0420 adopts a homodimeric hot-dog fold. The crystal structure suggests that HF0420 has enzymatic activity that involves a conserved histidine residue at the end of the central alpha-helix. Subsequent biochemical studies provide clues to the function of HP0420 and HF0420.


  • Organizational Affiliation
    • College of Pharmacy and Research Institute for Drug Development, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 609-735, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 32.13 kDa 
  • Atom Count: 2,128 
  • Modeled Residue Count: 261 
  • Deposited Residue Count: 290 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HP0420 homologue
A, B
145Helicobacter felisMutation(s): 0 
UniProt
Find proteins for D5MNX9 (Helicobacter felis)
Explore D5MNX9 
Go to UniProtKB:  D5MNX9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5MNX9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.185 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.302α = 90
b = 67.129β = 90
c = 70.216γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
CNSrefinement
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: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-12
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description