› 3rq5

X-ray diffraction
1.7Å resolution

Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with CoA

Released:
DOI: 10.2210/pdb3rq5/pdb
PDB entry 3rq5 coloured by chain, front view.
PDB entry 3rq5 coloured by chain, side view.
PDB entry 3rq5 coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Identification of unknown protein function using metabolite cocktail screening.
Shumilin IA, Cymborowski M, Chertihin O, Jha KN, Herr JC, Lesley SA, Joachimiak A, Minor W
Structure 20 1715-25 (2012)
PMID: 22940582

Function and Biology Details

Reaction catalysed: 
ADP + (6S)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine-dinucleotide = AMP + phosphate + NADH
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161104 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
ADP-dependent (S)-NAD(P)H-hydrate dehydratase Chain: A
Molecule details ›
Chain: A
Length: 279 amino acids
Theoretical weight: 30.18 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P94368 (Residues: 1-276; Coverage: 100%)
Gene names: BSU38720, nnrD, yxkO
Sequence domains: Carbohydrate kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

2 bound ligands:
Ligand COA 1 x COA
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: I422
Unit cell:
a: 91.765Å b: 91.765Å c: 169.498Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.153 0.178
Expression system: Escherichia coli BL21

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Citations

11 review citations

Zebrafish models of dyslipidemia: relevance to atherosclerosis and angiogenesis.
Fang et al. (2014)
10 more