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 
  • R-Value Observed: 0.119 

Starting Model: experimental
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This is version 1.5 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: https://doi.org/10.1111/j.1742-4658.2012.08506.x
  • Primary Citation of Related Structures:  
    2QMO, 3MLE, 3QXC, 3QXH, 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) 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dethiobiotin synthetase242Helicobacter pylori 26695Mutation(s): 0 
Gene Names: bioDhp0029HP_0029
EC: 6.3.3.3
UniProt
Find proteins for O24872 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O24872 
Go to UniProtKB:  O24872
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO24872
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
8AC
Query on 8AC

Download Ideal Coordinates CCD File 
B [auth A]8-aminooctanoic acid
C8 H17 N O2
UQXNEWQGGVUVQA-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ADP PDBBind:  3QXH Kd: 5800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.117 
  • R-Value Observed: 0.119 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.526α = 90
b = 37.967β = 101.15
c = 68.795γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-28
    Changes: Database references
  • Version 1.3: 2013-03-27
    Changes: Database references
  • Version 1.4: 2022-04-13
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-09-13
    Changes: Data collection, Refinement description