› 5h2g

X-ray diffraction
2Å resolution

Crystal structure of oxidized DapF from Corynebacterium glutamicum

Released:
DOI: 10.2210/pdb5h2g/pdb
PDB entry 5h2g coloured by chain, front view.
PDB entry 5h2g coloured by chain, side view.
PDB entry 5h2g coloured by chain, top view.
Source organism: Corynebacterium glutamicum ATCC 13032
Primary publication:
Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis.
Sagong HY, Kim KJ
Sci Rep 7 42318 (2017)
PMID: 28176858

Function and Biology Details

Reaction catalysed: 
LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185621 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diaminopimelate epimerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 283 amino acids
Theoretical weight: 30.05 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q8NP73 (Residues: 1-277; Coverage: 100%)
Gene names: Cgl1943, cg2129, dapF
Sequence domains: Diaminopimelate epimerase
Structure domains: Diaminopimelate Epimerase; Chain A, domain 1

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: I222
Unit cell:
a: 101.738Å b: 119.079Å c: 155.585Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.189 0.219
Expression system: Escherichia coli BL21

Quick links

Citations

3 review citations

Allosteric disulfides: Sophisticated molecular structures enabling flexible protein regulation.
Chiu et al. (2019)
2 more

1 mention without citation

Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis.
Sagong et al. (2017)