3,2-trans-enoyl-CoA isomerase (mitochondrial)

 

Delta3-delta2-enoyl CoA isomerase (enoyl-CoA isomerase) is a mitochondrial enzyme, in this case from human, catalyses the conversion of 3-cis-enoyl-CoA or 3-trans-enoyl-CoA into 2-trans-enoyl-CoA. This is involved in an auxiliary pathway of fatty acid degradation, and the product is subsequently metabolised further by other enzymes of the pathway.

Enoyl-CoA isomerases use fatty acyl substrates with side-chains ranging from C6 to C16. The reaction used as example uses a C12 compund as substrate

 

Reference Protein and Structure

Sequence
P42126 UniProt (5.3.3.8) IPR001753 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1sg4 - Crystal structure of human mitochondrial delta3-delta2-enoyl-CoA isomerase (1.3 Å) PDBe PDBsum 1sg4
Catalytic CATH Domains
3.90.226.10 CATHdb (see all for 1sg4)
Click To Show Structure

Enzyme Reaction (EC:5.3.3.8)

cis-dodec-3-enoyl-CoA(4-)
CHEBI:58543ChEBI
→
trans-dodec-2-enoyl-CoA(4-)
CHEBI:57330ChEBI
Alternative enzyme names: Delta(3)-cis-Delta(2)-trans-enoyl-CoA isomerase, Acetylene-allene isomerase, Dodecenoyl-CoA Delta-isomerase, Dodecenoyl-CoA Delta(3)-cis-Delta(2)-trans-isomerase, Delta(3),Delta(2)-enoyl-CoA isomerase, 3,2-trans-enoyl-CoA isomerase, ECI (gene name), Dodecenoyl-CoA isomerase, Dodecenoyl-CoA (3Z)-(2E)-isomerase,

Enzyme Mechanism

Introduction

This reaction proceeds via an E1cb mechanism in which Glu136 deprotonates the C2 atom of the substrate, forming the conjugate base. The thioester oxygen atom holds the negative charge, and is stabilised by the presence of an oxyanion hole formed by the amide groups of Leu77 and Gly111. As the carbonyl is reformed, the C4 atom of the product is protonated by Glu136.

Catalytic Residues Roles

UniProt PDB* (1sg4)
Leu108 (main-N), Gly153 (main-N) Leu66A (main-N), Gly111A (main-N) Forms the oxyanion hole that stabilises the negatively charged tetrahedral intermediate. hydrogen bond donor, electrostatic stabiliser
Glu178 Glu136A Acts as a general acid/base. proton donor, proton acceptor, polar/non-polar interaction
Asn177 Asn135A Activates Glu136 through hydrogen bonding, modifying its pKa so that it will be a better general acid/base. modifies pKa, 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

proton transfer, assisted keto-enol tautomerisation, native state of enzyme regenerated

References

  1. Partanen ST et al. (2004), J Mol Biol, 342, 1197-1208. The 1.3Å Crystal Structure of Human Mitochondrial Δ3-Δ2-Enoyl-CoA Isomerase Shows a Novel Mode of Binding for the Fatty Acyl Group. DOI:10.1016/j.jmb.2004.07.039. PMID:15351645.

Step 1. Glu136A deprotonates the substrate with concomitant tautomerisation to the enolate form, which is stabilised by an oxyanion hole composed of the main chain amides of Leu66A and Gly111A

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Leu66A (main-N) hydrogen bond donor, electrostatic stabiliser
Glu136A polar/non-polar interaction
Gly111A (main-N) hydrogen bond donor, electrostatic stabiliser
Asn135A modifies pKa, electrostatic stabiliser
Glu136A proton acceptor

Chemical Components

proton transfer, assisted keto-enol tautomerisation

Step 2. The oxyanion intermediate tautomerises to give product with the help of a proton donated by Glu136

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Leu66A (main-N) hydrogen bond donor, electrostatic stabiliser
Glu136A polar/non-polar interaction
Gly111A (main-N) hydrogen bond donor, electrostatic stabiliser
Asn135A modifies pKa, electrostatic stabiliser
Glu136A proton donor

Chemical Components

proton transfer, assisted keto-enol tautomerisation, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Glu136A deprotonates the substrate with concomitant tautomerisation to the enolate form, which is stabilised by an oxyanion hole composed of the main chain amides of Leu66A and Gly111A

Step 2. The oxyanion intermediate tautomerises to give product with the help of a proton donated by Glu136

Products.

Contributors

Daniel E. Almonacid, Sophie T. Williams, Gemma L. Holliday