1KLX | pdb_00001klx

Helicobacter pylori cysteine rich protein B (hcpB)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.238 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

The crystal structure of Helicobacter pylori cysteine-rich protein B reveals a novel fold for a penicillin-binding protein.

Luthy, L.Grutter, M.G.Mittl, P.R.

(2002) J Biological Chem 277: 10187-10193

  • DOI: https://doi.org/10.1074/jbc.M108993200
  • Primary Citation Related Structures: 
    1KLX

  • PubMed Abstract: 

    Colonization of the gastric mucosa with the spiral-shaped Gram-negative proteobacterium Helicobacter pylori is probably the most common chronic infection in humans. The genomes of H. pylori strains J99 and 26695 have been completely sequenced. Functional and three-dimensional structural information is available for less than one third of all open reading frames. We investigated the function and three-dimensional structure of a member from a family of cysteine-rich hypothetical proteins that are unique to H. pylori and Campylobacter jejuni. The structure of H. pylori cysteine-rich protein (Hcp) B possesses a modular architecture consisting of four alpha/alpha-motifs that are cross-linked by disulfide bridges. The Hcp repeat is similar to the tetratricopeptide repeat, which is frequently found in protein/protein interactions. In contrast to the tetratricopeptide repeat, the Hcp repeat is 36 amino acids long. HcpB is capable of binding and hydrolyzing 6-amino penicillinic acid and 7-amino cephalosporanic acid derivatives. The HcpB fold is distinct from the fold of any known penicillin-binding protein, indicating that the Hcp proteins comprise a new family of penicillin-binding proteins. The putative penicillin binding site is located in an amphipathic groove on the concave side of the molecule.


  • Organizational Affiliation
    • Biochemisches Institut, Universität Zürich, Winterthurer Strasse 190, 8057 Zürich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 15.37 kDa 
  • Atom Count: 1,218 
  • Modeled Residue Count: 133 
  • Deposited Residue Count: 138 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cysteine Rich Protein B138Helicobacter pyloriMutation(s): 0 
Gene Names: HP0336
EC: 3.5.2.6
UniProt
Find proteins for O25103 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25103 
Go to UniProtKB:  O25103
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25103
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.238 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.36α = 90
b = 51.36β = 90
c = 205.941γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Structure summary