› 8vkt

X-ray diffraction
1.4Å resolution

Crystallographic structure of dimetalated DapE from Enterococcus faecium

Released:
DOI: 10.2210/pdb8vkt/pdb
PDB entry 8vkt coloured by chain, front view.
PDB entry 8vkt coloured by chain, side view.
PDB entry 8vkt coloured by chain, top view.
Source organism: Enterococcus faecium
Primary publication:
The three-dimensional structure of DapE from Enterococcus faecium reveals new insights into DapE/ArgE subfamily ligand specificity.
Terrazas-López M, González-Segura L, Díaz-Vilchis A, Aguirre-Mendez KA, Lobo-Galo N, Martínez-Martínez A, Díaz-Sánchez ÁG
Int J Biol Macromol 132281 (2024)
PMID: 38740150

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-228896 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable succinyl-diaminopimelate desuccinylase Chain: A
Molecule details ›
Chain: A
Length: 402 amino acids
Theoretical weight: 43.98 KDa
Source organism: Enterococcus faecium
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A1S8KJG1 (Residues: 1-379; Coverage: 100%)
Gene names: B1P95_14080, GBM44_10270
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand GOL 2 x GOL
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2
Unit cell:
a: 131.822Å b: 44.914Å c: 78.024Å
α: 90° β: 104.28° γ: 90°
R-values:
R R work R free
0.155 0.154 0.176
Expression system: Escherichia coli BL21(DE3)

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