Crystal structure of the monoclinic form of alpha-carbonic anhydrase from the human pathogen Helicobacter pylori

Experimental Data Snapshot

  • Resolution: 1.52 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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Structure of alpha-carbonic anhydrase from the human pathogen Helicobacter pylori.

Compostella, M.E.Berto, P.Vallese, F.Zanotti, G.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1005-1011

  • DOI: https://doi.org/10.1107/S2053230X15010407
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of α-carbonic anhydrase, an enzyme present in the periplasm of Helicobacter pylori, a bacterium that affects humans and that is responsible for several gastric pathologies, is described. Two enzyme monomers are present in the asymmetric unit of the monoclinic space group P21, forming a dimer in the crystal. Despite the similarity of the enzyme structure to those of orthologues from other species, the H. pylori protein has adopted peculiar features in order to allow the bacterium to survive in the difficult environment of the human stomach. In particular, the crystal structure shows how the bacterium has corrected for the mutation of an essential amino acid important for catalysis using a negative ion from the medium and how it localizes close to the inner membrane in the periplasm. Since carbonic anhydrase is essential for the bacterial colonization of the host, it is a potential target for antibiotic drugs. The definition of the shape of the active-site entrance and cavity constitutes a basis for the design of specific inhibitors.

  • Organizational Affiliation

    Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, 35131 Padua, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-carbonic anhydrase
A, B
226Helicobacter pylori G27Mutation(s): 0 
Gene Names: HPG27_1129
Find proteins for B5Z8I0 (Helicobacter pylori (strain G27))
Explore B5Z8I0 
Go to UniProtKB:  B5Z8I0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5Z8I0
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
CL BindingDB:  4XFW Ki: min: 2.70e+6, max: 2.70e+6 (nM) from 2 assay(s)
SO4 BindingDB:  4XFW Ki: min: 8.20e+5, max: 8.20e+5 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.52 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.906α = 90
b = 95.905β = 92.92
c = 53.318γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
MIURItalyUnraveling structural and functional determinants behind Helicobacter pylori pathogenesis and persistence

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2015-08-19
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description