Resorcylate decarboxylase

 

γ-Resorcylate decarboxylase (γ-RSD) has evolved to catalyse the decarboxylation of 2,6-dihydroxybenzoate to resorcinol. This enzyme is of significant interest because of its potential for the production of γ-resorcylate and other benzoic acid derivatives under environmentally sustainable conditions. It contains a manganese ion and an aspartate in the active site responsible for the reaction. The reaction is reversible, but equilibrium greatly favors the decarboxylation reaction.

 

Reference Protein and Structure

Sequence
Q12BV1 UniProt IPR032465 (Sequence Homologues) (PDB Homologues)
Biological species
Polaromonas sp. JS666 (Bacteria) Uniprot
PDB
4qro - CRYSTAL STRUCTURE of DIHYDROXYBENZOIC ACID DECARBBOXYLASE BPRO_2061 (TARGET EFI-500288) FROM POLAROMONAS SP. JS666 WITH BOUND MANGANESE AND AN INHIBITOR, 2-NITRORESORCINOL (1.65 Å) PDBe PDBsum 4qro
Catalytic CATH Domains
3.20.20.140 CATHdb (see all for 4qro)
Cofactors
Manganese(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:4.1.1.103)

2,6-dihydroxybenzoate
CHEBI:131450ChEBI
+
hydron
CHEBI:15378ChEBI
→
carbon dioxide
CHEBI:16526ChEBI
+
resorcinol
CHEBI:27810ChEBI
Alternative enzyme names: GraF (gene name), TsdA (gene name),

Enzyme Mechanism

Introduction

In the proposed reaction mechanism, gamma-resorcylate binds 2,6-dihydroxybenzoate by direct coordination of the active site manganese ion to the carboxylate anion and one of the adjacent phenolic oxygens of the substrate. The enzyme subsequently catalyzes the transfer of a proton to C1 of gamma-resorcylate. This causes the decarboxylation of the substrate. This reaction is reversible but highly in favour of the decarboxylation reaction.

Catalytic Residues Roles

UniProt PDB* (4qro)
Asp287 Asp287G Acts as a proton donor to the substrate causing the decarboxylation. metal ligand, proton donor
His164, Glu8, Asp287, His10 His164G, Glu8G, Asp287G, His10G The residues responsible for manganese coordination. metal ligand
*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

proton transfer, intermediate formation, intermediate collapse, unimolecular elimination by the conjugate base, overall reactant used, intramolecular rearrangement, overall product formed

References

  1. Sheng X et al. (2018), Biochemistry, 57, 3167-3175. Mechanism and Structure of γ-Resorcylate Decarboxylase. DOI:https://doi.org/10.1021/acs.biochem.7b01213.
  2. Sheng X et al. (2018), Front Chem, 6,Reaction Mechanism and Substrate Specificity of Iso-orotate Decarboxylase: A Combined Theoretical and Experimental Study. DOI:https://doi.org/10.3389/fchem.2018.00608.
  3. Kasai D et al. (2015), Appl Environ Microbiol, 81, 7656-7665. γ-Resorcylate catabolic-pathway genes in the soil actinomycete Rhodococcus jostii RHA1. DOI:10.1128/AEM.02422-15. PMID:26319878.
  4. Goto M et al. (2006), J Biol Chem, 281, 34365-34373. Crystal structures of nonoxidative zinc-dependent 2,6-dihydroxybenzoate (gamma-resorcylate) decarboxylase from Rhizobium sp. strain MTP-10005. DOI:10.1074/jbc.M607270200. PMID:16963440.

Step 1. Asp287 protonates the C1 of the substrate. This forms an intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His164G metal ligand
Glu8G metal ligand
Asp287G metal ligand, proton donor
His10G metal ligand

Chemical Components

proton transfer, intermediate formation, intermediate collapse, ingold: unimolecular elimination by the conjugate base, overall reactant used

Step 2. The intermediate collapses with a bond rearrangement. The carboxylate leaves the substrate as carbon dioxide.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His164G metal ligand
Glu8G metal ligand
Asp287G metal ligand
His10G metal ligand

Chemical Components

intramolecular rearrangement, overall product formed
Download: Image, Marvin File

Step 1. Asp287 protonates the C1 of the substrate. This forms an intermediate.

Step 2. The intermediate collapses with a bond rearrangement. The carboxylate leaves the substrate as carbon dioxide.

Products.

Contributors

Marko Babić, Antonio Ribeiro