3QXH

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ADP and 8-aminocaprylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.117 

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:  2QMO, 3MLE, 3QXC, 3QXJ, 3QXS, 3QXX, 3QY0

  • 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
242Helicobacter pylori (strain ATCC 700392 / 26695)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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
8AC
Query on 8AC

Download SDF File 
Download CCD File 
A
8-aminooctanoic acid
8-aminocaprylic acid
C8 H17 N O2
UQXNEWQGGVUVQA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADPKd: 5800 nM BINDINGMOAD
ADPKd: 5800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.117 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.526α = 90.00
b = 37.967β = 101.15
c = 68.795γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
HKL-3000data reduction
HKL-3000data collection
MOLREPphasing
REFMACrefinement
HKL-3000phasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-28
    Type: Database references
  • Version 1.3: 2013-03-27
    Type: Database references