› 2yxx

X-ray diffraction
1.7Å resolution

Crystal structure analysis of Diaminopimelate decarboxylate (lysA)

Released:
DOI: 10.2210/pdb2yxx/pdb
PDB entry 2yxx coloured by chain, front view.
PDB entry 2yxx coloured by chain, side view.
PDB entry 2yxx coloured by chain, top view.
Source organism: Thermotoga maritima MSB8
Entry authors: Nakamura Y, Bessho Y, Padmanabhan B, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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 analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-194813 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diaminopimelate decarboxylase Chain: A
Molecule details ›
Chain: A
Length: 386 amino acids
Theoretical weight: 44.56 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9X1K5 (Residues: 1-386; Coverage: 100%)
Gene names: TM_1517, lysA
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand PLP 1 x PLP
No bound ligands
1 modified residue:
Ligand MSE 11 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: I222
Unit cell:
a: 87.818Å b: 98.276Å c: 109.304Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.189 0.22
Expression system: Escherichia coli

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