Protocatechuate 4,5-dioxygenase

 

The LigAB enzyme from Sphingomonas paucimobilis SYK-6 is a protocatechuate 4,5-dioxygenase, catalyses the ring-opening of protocatechuate (PCA) by oxidation to cleave the C4-C5 bond adjacent to the vicinal hydroxyl group. It belongs to the family of class III extradiol-type catecholic dioxygenase which is characterised by a ferrous iron in the active site. It has been identified as a key enzyme in the lignin-degradation pathway of Sphingomonas paucimobilis SYK-6.

 

Reference Protein and Structure

Sequences
P22635 UniProt (1.13.11.8)
P22636 UniProt (1.13.11.8) IPR034937 (Sequence Homologues) (PDB Homologues)
Biological species
Sphingobium sp. SYK-6 (Bacteria) Uniprot
PDB
1bou - THREE-DIMENSIONAL STRUCTURE OF LIGAB (2.2 Å) PDBe PDBsum 1bou
Catalytic CATH Domains
3.40.830.10 CATHdb (see all for 1bou)
Cofactors
Iron(3+) (1)
Click To Show Structure

Enzyme Reaction (EC:1.13.11.8)

dioxygen
CHEBI:15379ChEBI
+
3,4-dihydroxybenzoate
CHEBI:36241ChEBI
→
4-carboxy-2-hydroxy-cis,cis-muconate 6-semialdehyde(2-)
CHEBI:58358ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: Protocatechuate 4,5-oxygenase, Protocatechuic 4,5-dioxygenase, Protocatechuic 4,5-oxygenase, Protocatechuate:oxygen 4,5-oxidoreductase (decyclizing),

Enzyme Mechanism

Introduction

Based on the common features around the active sites of BphC, a class II extradiol-type catacholic dioxygenase, and LigAB, it was suggested that LigAB has the same catalytic mechanism as BphC. The 2 hydroxyl groups of PCA chelate the Fe(II) centre with only one proton lost upon binding of the substrate. Binding of the substrate anion to the Fe(II) activates it to bind dioxygen at the vacant sixth coordination site. O2 binding results in the transfer of charge from Fe(II) to O2, forming an Fe(III)-superoxide species. A subsequent shift of electron density from coordinates PCA to the iron centre enhances the nucleophilic attack of the nascent superoxide on the PCA ring to form an intermediate alkylperoxo moiety. Cleavage of the O-O bond, coupled with a ring insertion reaction with His195b as the base catalyst, forms a seven-membered lactone ring. Hydrolysis of the lactone ring yields a semialdehyde product.

Catalytic Residues Roles

UniProt PDB* (1bou)
His12, His61, Glu242 His12B, His61B, Glu242B His12, His61 and Glu242 are coordinated to the Fe(II) ion and are completely conserved among related enzymes (PMID: 1046715). These residues occupy equatorial positions around Fe(II) and, along with a water molecule, in the substrate-free form result in a distorted trigonal pyamid coordination sphere.
His195 His195B It acts as a base to deprotonate the C4-hydroxyl group in the reaction.
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Sugimoto K et al. (1999), Structure, 7, 953-965. Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions. DOI:10.1016/s0969-2126(99)80122-1. PMID:10467151.

Contributors

Mei Leung, Gemma L. Holliday, Amelia Brasnett