› 5ees

X-ray diffraction
2.15Å resolution

Crystal structure of DapB in complex with NADP+ from Corynebacterium glutamicum

Released:
DOI: 10.2210/pdb5ees/pdb
Model geometry
Fit model/data
PDB entry 5ees coloured by chain, front view.
PDB entry 5ees coloured by chain, side view.
PDB entry 5ees coloured by chain, top view.
Source organism: Corynebacterium glutamicum ATCC 13032
Primary publication:
Structural Insight into Dihydrodipicolinate Reductase from Corybebacterium glutamicum for Lysine Biosynthesis.
Sagong HY, Kim KJ
J Microbiol Biotechnol 26 226-32 (2016)
PMID: 26502738

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-154027 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-hydroxy-tetrahydrodipicolinate reductase Chain: A
Molecule details ›
Chain: A
Length: 247 amino acids
Theoretical weight: 25.92 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Escherichia coli
UniProt:
  • Canonical: P40110 (Residues: 2-248; Coverage: 100%)
Gene names: Cgl1973, cg2163, dapB
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAP 1 x NAP
2 bound ligands:
Ligand GOL 1 x GOL
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: I4122
Unit cell:
a: 107.969Å b: 107.969Å c: 172.049Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.179 0.211
Expression system: Escherichia coli

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Citations

6 citation in other articles

A new genome-scale metabolic model of Corynebacterium glutamicum and its application.
Zhang et al. (2017)
5 more

1 mention without citation

Crystal structure of dihydrodipicolinate reductase (PaDHDPR) from Paenisporosarcina sp. TG-14: structural basis for NADPH preference as a cofactor.
Lee et al. (2018)