Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members

FEBS J. 2012 Mar;279(6):1093-105. doi: 10.1111/j.1742-4658.2012.08506.x. Epub 2012 Feb 27.

Abstract

Dethiobiotin synthetase (DTBS) is involved in the biosynthesis of biotin in bacteria, fungi, and plants. As humans lack this pathway, DTBS is a promising antimicrobial drug target. We determined structures of DTBS from Helicobacter pylori (hpDTBS) bound with cofactors and a substrate analog, and described its unique characteristics relative to other DTBS proteins. Comparison with bacterial DTBS orthologs revealed considerable structural differences in nucleotide recognition. The C-terminal region of DTBS proteins, which contains two nucleotide-recognition motifs, differs greatly among DTBS proteins from different species. The structure of hpDTBS revealed that this protein is unique and does not contain a C-terminal region containing one of the motifs. The single nucleotide-binding motif in hpDTBS is similar to its counterpart in GTPases; however, isothermal titration calorimetry binding studies showed that hpDTBS has a strong preference for ATP. The structural determinants of ATP specificity were assessed with X-ray crystallographic studies of hpDTBS·ATP and hpDTBS·GTP complexes. The unique mode of nucleotide recognition in hpDTBS makes this protein a good target for H. pylori-specific inhibitors of the biotin synthesis pathway.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adenosine Triphosphate / metabolism
  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Carbon-Nitrogen Ligases / chemistry*
  • Carbon-Nitrogen Ligases / metabolism
  • Crystallography, X-Ray
  • Helicobacter pylori / enzymology*
  • Kinetics
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Sequence Alignment
  • Substrate Specificity

Substances

  • Bacterial Proteins
  • Adenosine Triphosphate
  • Carbon-Nitrogen Ligases
  • dethiobiotin synthetase

Associated data

  • PDB/2QMO
  • PDB/3MLE
  • PDB/3QXC
  • PDB/3QXH
  • PDB/3QXJ
  • PDB/3QXS
  • PDB/3QXX
  • PDB/3QY0