› 1sc9

X-ray diffraction
1.8Å resolution

Hydroxynitrile Lyase from Hevea brasiliensis in complex with the natural substrate acetone cyanohydrin

Released:
DOI: 10.2210/pdb1sc9/pdb
PDB entry 1sc9 coloured by chain, front view.
PDB entry 1sc9 coloured by chain, side view.
PDB entry 1sc9 coloured by chain, top view.
Source organism: Hevea brasiliensis
Primary publication:
Reaction mechanism of hydroxynitrile lyases of the alpha/beta-hydrolase superfamily: the three-dimensional structure of the transient enzyme-substrate complex certifies the crucial role of LYS236.
Gruber K, Gartler G, Krammer B, Schwab H, Kratky C
J Biol Chem 279 20501-10 (2004)
PMID: 14998991

Function and Biology Details

Reaction catalysed: 
An aliphatic (S)-hydroxynitrile = cyanide + an aliphatic aldehyde or ketone
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
homo dimer
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156603 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
(S)-hydroxynitrile lyase Chain: A
Molecule details ›
Chain: A
Length: 257 amino acids
Theoretical weight: 29.26 KDa
Source organism: Hevea brasiliensis
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P52704 (Residues: 1-257; Coverage: 100%)
Gene name: HNL
Sequence domains: alpha/beta hydrolase fold
Structure domains: alpha/beta hydrolase

Ligands and Environments

2 bound ligands:
Ligand SO4 2 x SO4
Ligand CNH 1 x CNH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: C2221
Unit cell:
a: 47.393Å b: 106.455Å c: 127.988Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.167 0.167 0.189
Expression system: Komagataella pastoris

Quick links

Citations

6 review citations

The alpha/beta-hydrolase fold 3DM database (ABHDB) as a tool for protein engineering.
Kourist et al. (2010)
5 more

2 mentions without citation

How the Same Core Catalytic Machinery Catalyzes 17 Different Reactions: the Serine-Histidine-Aspartate Catalytic Triad of α/β-Hydrolase Fold Enzymes.
Rauwerdink et al. (2015)
1 more