› 8d5d

X-ray diffraction
1.54Å resolution

Structure of Y430F D-ornithine/D-lysine decarboxylase complex with D-arginine

Released:
DOI: 10.2210/pdb8d5d/pdb
Model geometry
Fit model/data
PDB entry 8d5d coloured by chain, front view.
PDB entry 8d5d coloured by chain, side view.
PDB entry 8d5d coloured by chain, top view.
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Primary publication:
The Y430F mutant of Salmonella d-ornithine/d-lysine decarboxylase has altered stereospecificity and a putrescine allosteric activation site.
Phillips RS, Nguyen Hoang KN
Arch Biochem Biophys 731 109429 (2022)
PMID: 36265649

Function and Biology Details

Reaction catalysed: 
D-lysine = cadaverine + CO(2)
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-187297 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-ornithine/D-lysine decarboxylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 477 amino acids
Theoretical weight: 54.05 KDa
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8ZNC4 (Residues: 1-465; Coverage: 100%)
Gene names: STM2360, dokD
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand DMS 7 x DMS
Ligand 5DK 2 x 5DK
Ligand GOL 2 x GOL
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 141.77Å b: 49.54Å c: 139.56Å
α: 90° β: 115.93° γ: 90°
R-values:
R R work R free
0.162 0.161 0.193
Expression system: Escherichia coli BL21(DE3)

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