2QMO

Crystal structure of dethiobiotin synthetase (bioD) from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

Porebski, P.J.Klimecka, M.Chruszcz, M.Nicholls, R.A.Murzyn, K.Cuff, M.E.Xu, X.Cymborowski, M.Murshudov, G.N.Savchenko, A.Edwards, A.Minor, W.

(2012) Febs J. 279: 1093-1105

  • DOI: 10.1111/j.1742-4658.2012.08506.x
  • Primary Citation of Related Structures:  

  • PubMed 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) bo ...

    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.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dethiobiotin synthetase
A
220Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: bioD
EC: 6.3.3.3
Find proteins for O24872 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O24872
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.148 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 82.095α = 90.00
b = 37.454β = 101.48
c = 69.636γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
DMphasing
HKL-3000data collection
HKL-3000phasing
CCP4phasing
RESOLVEphasing
Omodel building
DMmodel building
MLPHAREphasing
SHELXDphasing
SHELXEmodel building
HKL-2000data reduction
ARP/wARPmodel building
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2012-03-28
    Type: Database references
  • Version 1.3: 2013-03-27
    Type: Database references