› 1tuf

X-ray diffraction
2.4Å resolution

Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi

Released:
DOI: 10.2210/pdb1tuf/pdb
PDB entry 1tuf coloured by chain, front view.
PDB entry 1tuf coloured by chain, side view.
PDB entry 1tuf coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor.
Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK
Structure 10 1499-508 (2002)
PMID: 12429091

Function and Biology Details

Reaction catalysed: 
Meso-2,6-diaminoheptanedioate = L-lysine + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-176628 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diaminopimelate decarboxylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 434 amino acids
Theoretical weight: 48.69 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q58497 (Residues: 5-438; Coverage: 99%)
Gene names: MJ1097, lysA
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand AZ1 2 x AZ1
1 modified residue:
Ligand LLP 2 x LLP

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25, CHESS BEAMLINE F2
Spacegroup: P6122
Unit cell:
a: 80.806Å b: 80.806Å c: 508.503Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.204 0.204 0.253
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Sphingolipid biosynthesis in man and microbes.
Harrison et al. (2018)
1 more

4 mentions without citation

Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis.
Peverelli et al. (2016)
3 more