› 4di8

X-ray diffraction
1.81Å resolution

CRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM SPHINGOMONAS PAUCIMOBILIS complexed with substrate at pH 8.5

Released:
DOI: 10.2210/pdb4di8/pdb
PDB entry 4di8 coloured by chain, front view.
PDB entry 4di8 coloured by chain, side view.
PDB entry 4di8 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 Chains: A, B
Molecule details ›
Chains: A, B
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

4 bound ligands:
Ligand 0GZ 2 x 0GZ
Ligand ACT 2 x ACT
Ligand 0GY 2 x 0GY
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21
Unit cell:
a: 74.348Å b: 52.131Å c: 76.539Å
α: 90° β: 93.73° γ: 90°
R-values:
R R work R free
0.158 0.157 0.187
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)
11 other articles

4 mentions without citation

Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes.
Jin et al. (2017)
3 more