› 3rtd

X-ray diffraction
2.3Å resolution

Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NADH and ADP.

Released:
DOI: 10.2210/pdb3rtd/pdb
PDB entry 3rtd coloured by chain, front view.
PDB entry 3rtd coloured by chain, side view.
PDB entry 3rtd coloured by chain, top view.
Source organisms:
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

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

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164004 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Bifunctional NAD(P)H-hydrate repair enzyme Nnr Chain: A
Molecule details ›
Chain: A
Length: 502 amino acids
Theoretical weight: 54.53 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9X024 (Residues: 1-490; Coverage: 100%)
Gene names: TM_0922, nnr
Sequence domains:
Structure domains:
Unknown peptide, probably from expression host Chain: B
Molecule details ›
Chain: B
Length: 7 amino acids
Theoretical weight: 807 Da
Source organism: Escherichia coli

Ligands and Environments

5 bound ligands:
Ligand K 1 x K
Ligand MG 1 x MG
Ligand NAI 1 x NAI
Ligand ADP 1 x ADP
Ligand NAX 1 x NAX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: I422
Unit cell:
a: 121.81Å b: 121.81Å c: 155.221Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.167 0.164 0.219
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

11 review citations

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