6WSB

Crystal structure of a betaine aldehyde dehydrogenase from Burkholderia pseudomallei bound to cofactor NAD

• PDB DOI:  https://doi.org/10.2210/pdb6WSB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia pseudomallei 1710b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-30 Released: 2020-05-20 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.169 
• R-Value Work: 0.144 
• R-Value Observed: 0.146 

Literature

Crystal structure of betaine aldehyde dehydrogenase from Burkholderia pseudomallei.

Beard, D.K., Subramanian, S., Abendroth, J., Dranow, D.M., Edwards, T.E., Myler, P.J., Asojo, O.A.

(2022) Acta Crystallogr F Struct Biol Commun 78: 45-51

• PubMed: 35102892 
• DOI: https://doi.org/10.1107/S2053230X21013455
• Primary Citation of Related Structures:  
  6WSA, 6WSB


• PubMed Abstract: 
  

Burkholderia pseudomallei infection causes melioidosis, which is often fatal if untreated. There is a need to develop new and more effective treatments for melioidosis. This study reports apo and cofactor-bound crystal structures of the potential drug target betaine aldehyde dehydrogenase (BADH) from B. pseudomallei. A structural comparison identified similarities to BADH from Pseudomonas aeruginosa which is inhibited by the drug disulfiram. This preliminary analysis could facilitate drug-repurposing studies for B. pseudomallei.

---

Organizational Affiliation: 

Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 107.78 kDa 
• Atom Count: 9,024 
• Modelled Residue Count: 978 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD/NADP-dependent betaine aldehyde dehydrogenase	A, B	496	Burkholderia pseudomallei 1710b	Mutation(s): 0  Gene Names: betB, BURPS1710b_A0376 EC: 1.2.1.8
UniProt
Find proteins for Q3JLL8 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JLL8  Go to UniProtKB:  Q3JLL8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL	D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.169 
• R-Value Work: 0.144 
• R-Value Observed: 0.146 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M36WSB

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.27	α = 90
b = 156.7	β = 90
c = 76.23	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references