› 4ppz

X-ray diffraction
2Å resolution

Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Neisseria meningitidis MC58

Released:
DOI: 10.2210/pdb4ppz/pdb
PDB entry 4ppz coloured by chain, front view.
PDB entry 4ppz coloured by chain, side view.
PDB entry 4ppz coloured by chain, top view.
Source organism: Neisseria meningitidis MC58
Primary publication:
Inhibition of the dapE-Encoded N-Succinyl-L,L-diaminopimelic Acid Desuccinylase from Neisseria meningitidis by L-Captopril.
Starus A, Nocek B, Bennett B, Larrabee JA, Shaw DL, Sae-Lee W, Russo MT, Gillner DM, Makowska-Grzyska M, Joachimiak A, Holz RC
Biochemistry 54 4834-44 (2015)
PMID: 26186504

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
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-191694 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Succinyl-diaminopimelate desuccinylase Chain: A
Molecule details ›
Chain: A
Length: 381 amino acids
Theoretical weight: 41.37 KDa
Source organism: Neisseria meningitidis MC58
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9JYL2 (Residues: 1-381; Coverage: 100%)
Gene names: NMB1530, dapE
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2221
Unit cell:
a: 116.963Å b: 151.655Å c: 55.464Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.174 0.208
Expression system: Escherichia coli

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Citations

9 citation in other articles

FDA-approved thiol-reacting drugs that potentially bind into the SARS-CoV-2 main protease, essential for viral replication.
Lobo-Galo et al. (2021)
8 more

1 mention without citation

Inhibition of the dapE-Encoded N-Succinyl-L,L-diaminopimelic Acid Desuccinylase from Neisseria meningitidis by L-Captopril.
Starus et al. (2015)