Methylglutaconyl-CoA hydratase

 

AU binding protein/enoyl-coA hydratase (AUH) is from Homo sapiens. It binds to AUUU repeats in RNA and also weakly catalyses the hydration of 2-trans-enoyl-coenzyme A (enoyl-coA). The hydration of enoyl-coA is necessary for the break-down of fatty acids. [PMID:12655555]. This entry represents the 3-hydroxy-3-methylglutaconyl- CoA dehydratase activity. It is a member of the crotonase superfamily.

 

Reference Protein and Structure

Sequence
Q13825 UniProt (4.2.1.18, 4.2.1.56) IPR001753 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1hzd - CRYSTAL STRUCTURE OF HUMAN AUH PROTEIN, AN RNA-BINDING HOMOLOGUE OF ENOYL-COA HYDRATASE (2.2 Å) PDBe PDBsum 1hzd
Catalytic CATH Domains
3.90.226.10 CATHdb (see all for 1hzd)
Click To Show Structure

Enzyme Reaction (EC:4.2.1.18)

trans-3-methylglutaconyl-CoA(5-)
CHEBI:57346ChEBI
+
water
CHEBI:15377ChEBI
→
(3S)-3-hydroxy-3-methylglutaryl-CoA(5-)
CHEBI:43074ChEBI
Alternative enzyme names: 3-methylglutaconyl CoA hydratase, Methylglutaconase, Methylglutaconyl coenzyme A hydratase, (S)-3-hydroxy-3-methylglutaryl-CoA hydro-lyase,

Enzyme Mechanism

Introduction

The substrate is activated by the polarisation of the enone pi-system through a strong hydrogen bond between the backbone amide of Gly186 and the thioester carbonyl of the bound enoyl-CoA. Glu189 acts as a general base and activates a water molecule for attack on the C3 atom. The C2 atom then accepts a proton from protonated Glu209.

Catalytic Residues Roles

UniProt PDB* (1hzd)
Glu209 Glu209(142)A Glu 209 acts as an acid and donates a proton to the C2 atom of the product. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
Gly186 (main-N), Ala141 (main-N) Gly186(119)A (main-N), Ala141(74)A (main-N) Activates the substrate by polarisation of the enone pi-system through a strong hydrogen bond between its backbone amide and the thioester carbonyl of the bound enoyl-coA hydrogen bond donor, electrostatic stabiliser
Glu189 Glu189(122)A Glu 189 acts as a general base and activates a water molecule for nucleophilic attack on the C3 atom. hydrogen bond acceptor
*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, bimolecular nucleophilic addition, overall reactant used, intermediate formation, assisted keto-enol tautomerisation, intermediate terminated, overall product formed, native state of enzyme regenerated

References

  1. Kurimoto K et al. (2001), Structure, 9, 1253-1263. Crystal Structure of Human AUH Protein, a Single-Stranded RNA Binding Homolog of Enoyl-CoA Hydratase. DOI:10.1016/s0969-2126(01)00686-4. PMID:11738050.
  2. Zhang Y et al. (2017), 75, 494-. Theoretical Insight into the Catalytic Mechanism of Enoyl-CoA Hydratase. DOI:10.6023/A16100559.
  3. Bock T et al. (2016), Chembiochem, 17, 1658-1664. The Structure of LiuC, a 3-Hydroxy-3-Methylglutaconyl CoA Dehydratase Involved in Isovaleryl-CoA Biosynthesis in Myxococcus xanthus, Reveals Insights into Specificity and Catalysis. DOI:10.1002/cbic.201600225. PMID:27271456.
  4. Mack M et al. (2006), FEBS J, 273, 2012-2022. Biochemical characterization of human 3-methylglutaconyl-CoA hydratase and its role in leucine metabolism. DOI:10.1111/j.1742-4658.2006.05218.x. PMID:16640564.
  5. Ly TB et al. (2003), Hum Mutat, 21, 401-407. Mutations in theAUH gene cause 3-methylglutaconic aciduria type I. DOI:10.1002/humu.10202. PMID:12655555.
  6. Agnihotri G et al. (2003), Bioorg Med Chem, 34, 9-20. Enoyl-CoA Hydratase: Reaction, Mechanism, and Inhibition. DOI:10.1002/chin.200314288. PMID:12467702.
  7. Hofstein HA et al. (1999), Biochemistry, 38, 9508-9516. Role of Glutamate 144 and Glutamate 164 in the Catalytic Mechanism of Enoyl-CoA Hydratase†. DOI:10.1021/bi990506y. PMID:10413528.

Step 1. Glu209 abstracts a proton from water, with the concomitant attack of the hydroxyl group to C3 in the substrate. This is facilitated by the binding of the thioester oxygen atom to an oxyanion hole formed by the peptide nitrogens of Ala141 and of Gly186.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gly186(119)A (main-N) electrostatic stabiliser, hydrogen bond donor
Ala141(74)A (main-N) electrostatic stabiliser, hydrogen bond donor
Glu209(142)A hydrogen bond acceptor
Glu189(122)A hydrogen bond acceptor
Glu209(142)A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, overall reactant used, intermediate formation

Step 2. The oxyanion intermediate tautomerises to give product with the help of a proton donated by Glu209

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ala141(74)A (main-N) hydrogen bond donor, electrostatic stabiliser
Glu189(122)A hydrogen bond acceptor
Glu209(142)A hydrogen bond donor
Gly186(119)A (main-N) hydrogen bond donor, electrostatic stabiliser
Glu209(142)A proton donor

Chemical Components

proton transfer, assisted keto-enol tautomerisation, intermediate terminated, overall product formed, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Glu209 abstracts a proton from water, with the concomitant attack of the hydroxyl group to C3 in the substrate. This is facilitated by the binding of the thioester oxygen atom to an oxyanion hole formed by the peptide nitrogens of Ala141 and of Gly186.

Step 2. The oxyanion intermediate tautomerises to give product with the help of a proton donated by Glu209

Products.

Contributors

Daniel E. Almonacid, Sophie T. Williams, Ellie Wright, Gemma L. Holliday, James Willey