› 2zm9

X-ray diffraction
1.5Å resolution

Structure of 6-Aminohexanoate-dimer Hydrolase, A61V/S112A/A124V/R187S/F264C/G291R/G338A/D370Y mutant (Hyb-S4M94) with Substrate

Released:
DOI: 10.2210/pdb2zm9/pdb
PDB entry 2zm9 coloured by chain, front view.
PDB entry 2zm9 coloured by chain, side view.
PDB entry 2zm9 coloured by chain, top view.
Source organism: Paenarthrobacter ureafaciens
Primary publication:
Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a beta-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase.
Ohki T, Shibata N, Higuchi Y, Kawashima Y, Takeo M, Kato D, Negoro S
Protein Sci 18 1662-73 (2009)
PMID: 19521995

Function and Biology Details

Reaction catalysed: 
(N-(6-aminohexanoyl))(n) + H(2)O = (N-(6-aminohexanoyl))(n-1) + 6-aminohexanoate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139359 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
6-aminohexanoate-dimer hydrolase Chain: A
Molecule details ›
Chain: A
Length: 392 amino acids
Theoretical weight: 42.93 KDa
Source organism: Paenarthrobacter ureafaciens
Expression system: Escherichia coli
UniProt:
  • Canonical: P07061 (Residues: 1-28, 61-63, 190-208; Coverage: 13%)
  • Canonical: P07062 (Residues: 29-60, 64-189, 209-392; Coverage: 87%)
Gene names: nylB, nylB'
Sequence domains: Beta-lactamase
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand SO4 3 x SO4
Ligand ACA 2 x ACA
Ligand MES 2 x MES
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P3221
Unit cell:
a: 96.508Å b: 96.508Å c: 113.139Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.178 0.178 0.192
Expression system: Escherichia coli

Quick links

Citations

9 citation in other articles

Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis.
Nannemann et al. (2011)
8 more

1 mention without citation

Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a beta-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase.
Ohki et al. (2009)