› 3isz

X-ray diffraction
2Å resolution

Crystal structure of mono-zinc form of succinyl-diaminopimelate desuccinylase from Haemophilus influenzae

Released:
DOI: 10.2210/pdb3isz/pdb
PDB entry 3isz coloured by chain, front view.
PDB entry 3isz coloured by chain, side view.
PDB entry 3isz coloured by chain, top view.
Source organism: Haemophilus influenzae Rd KW20
Primary publication:
Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase.
Nocek BP, Gillner DM, Fan Y, Holz RC, Joachimiak A
J Mol Biol 397 617-26 (2010)
PMID: 20138056

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:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155183 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Succinyl-diaminopimelate desuccinylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 377 amino acids
Theoretical weight: 41.4 KDa
Source organism: Haemophilus influenzae Rd KW20
Expression system: Escherichia coli
UniProt:
  • Canonical: P44514 (Residues: 1-377; Coverage: 100%)
Gene names: HI_0102, dapE
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 45.176Å b: 95.709Å c: 181.179Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.202 0.254
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Lysine biosynthesis in bacteria: a metallodesuccinylase as a potential antimicrobial target.
Gillner et al. (2013)
1 more

4 mentions without citation

Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase.
Nocek et al. (2010)
3 more