Glutaconyl-CoA decarboxylase

 

Bacterial Glutaconyl-CoA decarboxylase is an unusual ion transport holozyme, which uses the free energy released from the decarboxylation of glutaconyl CoA to crotonyl CoA in order to power the active transport of sodium ions into the periplasm. The carboxyl transferase subunit, GCDalpha is responsible for the first step in this process whereby the transfer of carbon dioxide to the biotin cofactor on GCDalpha is carried out. This subunit displays structural homology to the family of crotonases such as methylmalonoyl CoA decarboxylase, but little sequence identity, so although it clearly shares a common ancestor, divergence is likely to have occurred a long time in the past.

 

Reference Protein and Structure

Sequence
Q06700 UniProt (7.2.4.5) IPR034733 (Sequence Homologues) (PDB Homologues)
Biological species
Acidaminococcus fermentans DSM 20731 (Bacteria) Uniprot
PDB
1pix - Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme A decarboxylase (2.2 Å) PDBe PDBsum 1pix
Catalytic CATH Domains
3.90.226.10 CATHdb (see all for 1pix)
Cofactors
Biotinate (1)
Click To Show Structure

Enzyme Reaction (EC:7.2.4.5)

trans-4-carboxybut-2-enoyl-CoA(5-)
CHEBI:57353ChEBI
+
hydron
CHEBI:15378ChEBI
→
crotonoyl-CoA(4-)
CHEBI:57332ChEBI
+
carbon dioxide
CHEBI:16526ChEBI
Alternative enzyme names: Glutaconyl coenzyme A decarboxylase, Pent-2-enoyl-CoA carboxy-lyase, 4-carboxybut-2-enoyl-CoA carboxy-lyase,

Enzyme Mechanism

Introduction

In the first stage of the reaction, the decarboxylation of glutaconyl coA occurs spontaneously, forming an enolate intermediate stabilised by an oxyanion hole composed of Gly 194 and Val 151. Protonation of this enolate occurs with biotin acting as the general acid, resulting in the crotonyl CoA product and the enolate form of biotin, stabilised by an oxyanion hole composed of Ile 415 and Ala 457. The enolate form of biotin is thus able to act as a nucleophile to attack the CO2 previously liberated thus forming the carboxylated biotin.

Catalytic Residues Roles

UniProt PDB* (1pix)
Gly195 (main-N) Gly194(195)A (main-N) As part of an oxyanion hole with Val 151 acts to stabilise the crotonyl coA enolate intermediate, thus facilitating the initial decarboxylation. electrostatic stabiliser
Val152 (main-N) Val151(152)A (main-N) As part of an oxyanion hole with Gly 194 acts to stabilise the crotonyl coA enolate intermediate, thus facilitating the initial decarboxylation. electrostatic stabiliser
Ile418 (main-N) Ile417(418)B (main-N) As part of an oxyanion hole with Ala 457 acts to stabilise the biotin enolate intermediate, thus allowing biotin to donate a proton to crotonyl coA, and to act as a nucleophile towards CO2 electrostatic stabiliser
Ala458 (main-N) Ala457(458)B (main-N) As part of an oxyanion hole with Ile 417 acts to stabilise the biotin enolate intermediate, thus allowing biotin to donate a proton to crotonyl coA, and to act as a nucleophile towards CO2 electrostatic stabiliser
*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

decarboxylation, overall reactant used, overall product formed, proton transfer, cofactor used, aldol addition, native state of cofactor is not regenerated, bimolecular nucleophilic addition

References

  1. Wendt KS et al. (2003), EMBO J, 22, 3493-3502. Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase. DOI:10.1093/emboj/cdg358. PMID:12853465.

Step 1. Glutaconyl-CoA is decarboxylated forming a crotonyl coA intermediate which is stabilized by Val151 and Gly194.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Val151(152)A (main-N) electrostatic stabiliser
Gly194(195)A (main-N) electrostatic stabiliser

Chemical Components

decarboxylation, overall reactant used, overall product formed

Step 2. The crotonyl coA intermediate accepts a proton from the biotin cofactor, forming a biotinate which is stabilized by Ile 417 and Ala 457.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Val151(152)A (main-N) electrostatic stabiliser
Gly194(195)A (main-N) electrostatic stabiliser
Ile417(418)B (main-N) electrostatic stabiliser
Ala457(458)B (main-N) electrostatic stabiliser

Chemical Components

proton transfer, cofactor used

Step 3. Nucelophilic attack from the biotinate leads to it becoming carboxylated.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ile417(418)B (main-N) electrostatic stabiliser
Ala457(458)B (main-N) electrostatic stabiliser

Chemical Components

aldol addition, native state of cofactor is not regenerated, ingold: bimolecular nucleophilic addition
Download: Image, Marvin File

Step 1. Glutaconyl-CoA is decarboxylated forming a crotonyl coA intermediate which is stabilized by Val151 and Gly194.

Step 2. The crotonyl coA intermediate accepts a proton from the biotin cofactor, forming a biotinate which is stabilized by Ile 417 and Ala 457.

Step 3. Nucelophilic attack from the biotinate leads to it becoming carboxylated.

Products.

Contributors

Peter Sarkies, Gemma L. Holliday, James Willey