› 3n2o

X-ray diffraction
2.3Å resolution

X-ray crystal structure of arginine decarboxylase complexed with Arginine from Vibrio vulnificus

Released:
DOI: 10.2210/pdb3n2o/pdb
PDB entry 3n2o coloured by chain, front view.
PDB entry 3n2o coloured by chain, side view.
PDB entry 3n2o coloured by chain, top view.
Source organism: Vibrio vulnificus YJ016
Primary publication:
Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine.
Deng X, Lee J, Michael AJ, Tomchick DR, Goldsmith EJ, Phillips MA
J Biol Chem 285 25708-19 (2010)
PMID: 20534592

Function and Biology Details

Reaction catalysed: 
L-arginine = agmatine + 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-181725 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Biosynthetic arginine decarboxylase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 648 amino acids
Theoretical weight: 73.64 KDa
Source organism: Vibrio vulnificus YJ016
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7MK24 (Residues: 1-640; Coverage: 100%)
Gene names: VV1986, speA
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand PLP 4 x PLP
1 bound ligand:
Ligand AG2 4 x AG2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 101.648Å b: 119.365Å c: 121.84Å
α: 90° β: 96.3° γ: 90°
R-values:
R R work R free
0.196 0.179 0.239
Expression system: Escherichia coli

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Citations

1 review citation

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently.
Currin et al. (2015)
15 other articles

5 mentions without citation

Evolution and multiplicity of arginine decarboxylases in polyamine biosynthesis and essential role in Bacillus subtilis biofilm formation.
Burrell et al. (2010)
4 more