Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.19 kDa 
• Atom Count: 2282 
• Modelled Residue Count: 224 
• Deposited Residue Count: 242 
• Unique protein chains: 1

3QXH

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

• PDB DOI: 10.2210/pdb3QXH/pdb

• Classification: LIGASE
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-03-01 Released: 2011-03-30 
• Deposition Author(s): Porebski, P.J., Klimecka, M.M., Chruszcz, M., Murzyn, K., Minor, C., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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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 

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

• PubMed: 22284390 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dethiobiotin synthetase	A	242	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: bioD, hp0029, HP_0029 EC: 6.3.3.3
UniProt
Find proteins for O24872 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O24872  Go to UniProtKB:  O24872

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
8AC	B [auth A]	8-aminooctanoic acid C8 H17 N O2 UQXNEWQGGVUVQA-UHFFFAOYSA-N
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	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	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ADP	Binding MOAD:  3QXH	Kd: 5800 (nM) from 1 assay(s)
	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 = 81.526	α = 90
b = 37.967	β = 101.15
c = 68.795	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-01 
• Released Date: 2011-03-30 
Deposition Author(s): Porebski, P.J., Klimecka, M.M., Chruszcz, M., Murzyn, K., Minor, C., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• 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