› 4op4

X-ray diffraction
1.65Å resolution

Crystal structure of the catalytic domain of DapE protein from V.cholerea in the Zn bound form

Released:
DOI: 10.2210/pdb4op4/pdb
PDB entry 4op4 coloured by chain, front view.
PDB entry 4op4 coloured by chain, side view.
PDB entry 4op4 coloured by chain, top view.
Source organism: Vibrio cholerae O1 biovar El Tor str. N16961
Primary publication:
The dimerization domain in DapE enzymes is required for catalysis.
Nocek B, Starus A, Makowska-Grzyska M, Gutierrez B, Sanchez S, Jedrzejczak R, Mack JC, Olsen KW, Joachimiak A, Holz RC
PLoS One 9 e93593 (2014)
PMID: 24806882

Function and Biology Details

Reaction catalysed: 
N-succinyl-LL-2,6-diaminoheptanedioate + H(2)O = succinate + LL-2,6-diaminoheptanedioate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192023 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Succinyl-diaminopimelate desuccinylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 268 amino acids
Theoretical weight: 28.68 KDa
Source organism: Vibrio cholerae O1 biovar El Tor str. N16961
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9KQ52 (Residues: 2-181, 295-377; Coverage: 70%)
Gene names: VC_2152, dapE
Sequence domains: Peptidase family M20/M25/M40
Structure domains: Zn peptidases

Ligands and Environments

4 bound ligands:
Ligand EDO 5 x EDO
Ligand ZN 4 x ZN
Ligand GOL 3 x GOL
Ligand BU1 6 x BU1
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P32
Unit cell:
a: 49.898Å b: 49.898Å c: 231.762Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.145 0.141 0.166
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 citation in other articles

Evolution of plant δ(1)-pyrroline-5-carboxylate reductases from phylogenetic and structural perspectives.
Forlani et al. (2015)
6 more

2 mentions without citation

Negative Epistasis and Evolvability in TEM-1 β-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder.
Dellus-Gur et al. (2015)
1 more