3IBX

Crystal structure of F47Y variant of TenA (HP1287) from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

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This is version 1.3 of the entry. See complete history


Literature

Structural and mutational analysis of TenA protein (HP1287) from the Helicobacter pylori thiamin salvage pathway - evidence of a different substrate specificity.

Barison, N.Cendron, L.Trento, A.Angelini, A.Zanotti, G.

(2009) FEBS J 276: 6227-6235

  • DOI: https://doi.org/10.1111/j.1742-4658.2009.07326.x
  • Primary Citation of Related Structures:  
    3IBX

  • PubMed Abstract: 

    HP1287 (tenA) from Helicobacter pylori is included among the genes that play a relevant role in bacterium colonization and persistence. The gene has been cloned and its product, protein TenA, has been expressed and purified. The crystal structures of the wild-type protein and the mutant F47Y have been determined at resolutions of 2.7 and 2.4 A, respectively. The molecular model, a homotetramer with 222 symmetry, shows that the H. pylori TenA structure belongs to the thiaminase II class of proteins. These enzymes were recently found to be involved in a salvage pathway for the synthesis of the thiamin precursor hydroxypyrimidine, which constitutes a building block in thiamin biosynthesis, in particular in bacteria living in the soil. By contrast, enzymatic measurements on TenA from H. pylori indicate that the activity on the putative substrate 4-amino-5-aminomethyl-2-methylpyrimidine is very modest. Moreover, in the present study, we demonstrate that the mutation at residue 47, a position where a phenylalanine occurs in all the strains of H. pylori sequenced to date, is not sufficient to explain the very low catalytic activity toward the expected substrate. As a result of differences in the colonization environment of H. pylori as well as the TenA structural and catalytic peculiar features, we suggest a possible pivotal role for the H. pylori enzyme in the thiamin biosynthetic route, which is in agreement with the relevance of this protein in the stomach colonization process.


  • Organizational Affiliation

    Department of Biological Chemistry, University of Padua, Italy.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative thiaminase IIA,
B [auth D]
221Helicobacter pyloriMutation(s): 1 
Gene Names: tenAHP1287
EC: 3.5.99.2
UniProt
Find proteins for A8KRL3 (Helicobacter pylori)
Explore A8KRL3 
Go to UniProtKB:  A8KRL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8KRL3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.728α = 90
b = 148.728β = 90
c = 233.566γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description