› 8d5r

X-ray diffraction
1.44Å resolution

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

Released:
DOI: 10.2210/pdb8d5r/pdb
PDB entry 8d5r coloured by chain, front view.
PDB entry 8d5r coloured by chain, side view.
PDB entry 8d5r 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

7 bound ligands:
Ligand DMS 4 x DMS
Ligand ORX 2 x ORX
Ligand ACT 2 x ACT
Ligand NA 3 x NA
Ligand CL 2 x CL
Ligand PUT 1 x PUT
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 141.53Å b: 50.2Å c: 140.28Å
α: 90° β: 116° γ: 90°
R-values:
R R work R free
0.165 0.165 0.19
Expression system: Escherichia coli BL21(DE3)

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