› 1ynh

X-ray diffraction
1.95Å resolution

Crystal Structure of N-Succinylarginine Dihydrolase, AstB, bound to Substrate and Product, an Enzyme from the Arginine Catabolic Pathway of Escherichia coli

Released:
DOI: 10.2210/pdb1ynh/pdb
PDB entry 1ynh coloured by chain, front view.
PDB entry 1ynh coloured by chain, side view.
PDB entry 1ynh coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystal structure of N-succinylarginine dihydrolase AstB, bound to substrate and product, an enzyme from the arginine catabolic pathway of Escherichia coli.
Tocilj A, Schrag JD, Li Y, Schneider BL, Reitzer L, Matte A, Cygler M
J Biol Chem 280 15800-8 (2005)
PMID: 15703173

Function and Biology Details

Reaction catalysed: 
N(2)-succinyl-L-arginine + 2 H(2)O = N(2)-succinyl-L-ornithine + 2 NH(3) + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160067 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-succinylarginine dihydrolase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 458 amino acids
Theoretical weight: 50.56 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P76216 (Residues: 2-447; Coverage: 100%)
Gene names: JW1734, astB, b1745, ydjT
Sequence domains: Succinylarginine dihydrolase
Structure domains: Succinylarginine dihydrolase

Ligands and Environments

2 bound ligands:
Ligand K 4 x K
Ligand SUO 4 x SUO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 54.862Å b: 166.915Å c: 185.894Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.219 0.246
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Mechanistic similarity and diversity among the guanidine-modifying members of the pentein superfamily.
Linsky et al. (2010)
1 more

1 mention without citation

Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold.
Koike et al. (2009)