› 5tem

X-ray diffraction
2.2Å resolution

Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibrio vulnificus with 2,6 Pyridine Dicarboxylic and NADH

Released:
DOI: 10.2210/pdb5tem/pdb
PDB entry 5tem coloured by chain, front view.
PDB entry 5tem coloured by chain, side view.
PDB entry 5tem coloured by chain, top view.
Source organism: Vibrio vulnificus CMCP6
Primary publication:
Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.
Pote S, Kachhap S, Mank NJ, Daneshian L, Klapper V, Pye S, Arnette AK, Shimizu LS, Borowski T, Chruszcz M
Biochim Biophys Acta Gen Subj 1865 129750 (2021)
PMID: 32980502

Function and Biology Details

Reaction catalysed: 
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)(+) + H(2)O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184046 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-hydroxy-tetrahydrodipicolinate reductase Chains: A, C
Molecule details ›
Chains: A, C
Length: 269 amino acids
Theoretical weight: 28.67 KDa
Source organism: Vibrio vulnificus CMCP6
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8DEM0 (Residues: 1-269; Coverage: 100%)
Gene names: VV1_0567, dapB
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
2 bound ligands:
Ligand PDC 2 x PDC
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21212
Unit cell:
a: 80.639Å b: 112.588Å c: 62.432Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.191 0.224
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 mentions without citation

Impact of an N-terminal Polyhistidine Tag on Protein Thermal Stability.
Booth et al. (2018)
1 more