› 3ic1

X-ray diffraction
2.3Å resolution

Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Haemophilus influenzae

Released:
DOI: 10.2210/pdb3ic1/pdb
PDB entry 3ic1 coloured by chain, front view.
PDB entry 3ic1 coloured by chain, side view.
PDB entry 3ic1 coloured by chain, top view.
Source organism: Haemophilus influenzae
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
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P44514 (Residues: 1-377; Coverage: 100%)
Gene names: HI_0102, dapE
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand GOL 2 x GOL
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 44.697Å b: 95.751Å c: 185.426Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.194 0.25
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

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

8 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)
7 more