› 4di9

X-ray diffraction
1.35Å resolution

CRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM SPHINGOMONAS PAUCIMOBILIS complexed with substrate at pH 6.5

Released:
DOI: 10.2210/pdb4di9/pdb
PDB entry 4di9 coloured by chain, front view.
PDB entry 4di9 coloured by chain, side view.
PDB entry 4di9 coloured by chain, top view.
Source organism: Sphingomonas paucimobilis
Primary publication:
Structure and catalytic mechanism of LigI: insight into the amidohydrolase enzymes of cog3618 and lignin degradation.
Hobbs ME, Malashkevich V, Williams HJ, Xu C, Sauder JM, Burley SK, Almo SC, Raushel FM
Biochemistry 51 3497-507 (2012)
PMID: 22475079

Function and Biology Details

Reaction catalysed: 
2-oxo-2H-pyran-4,6-dicarboxylate + H(2)O = (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131490 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-pyrone-4,6-dicarboxylate hydrolase Chain: A
Molecule details ›
Chain: A
Length: 303 amino acids
Theoretical weight: 33.99 KDa
Source organism: Sphingomonas paucimobilis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O87170 (Residues: 2-293; Coverage: 100%)
Gene names: SLG_12570, ligI
Sequence domains: Amidohydrolase
Structure domains: Metal-dependent hydrolases

Ligands and Environments

2 bound ligands:
Ligand 0GY 1 x 0GY
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: C2
Unit cell:
a: 73.552Å b: 50.952Å c: 73.346Å
α: 90° β: 91.86° γ: 90°
R-values:
R R work R free
0.161 0.16 0.183
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism.
Kamimura et al. (2017)
13 other articles

2 mentions without citation

Carboxylic ester hydrolases: Classification and database derived from their primary, secondary, and tertiary structures.
Chen et al. (2016)
1 more