L-carnitine CoA-transferase

 

The enzymes required for the metabolism of L-carnitine in Escherichia coli is encoded by the cai operon. CaiB, a class III CoA transferase, alongside formyl-CoA transferase. CaiB catalyses the reversible transfer of the CoA group from crotonobetainyl-CoA to L-carnitine.

 

Reference Protein and Structure

Sequence
P31572 UniProt (2.8.3.21) IPR023452 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1xvt - Crystal Structure of Native CaiB in complex with coenzyme A (2.3 Å) PDBe PDBsum 1xvt
Catalytic CATH Domains
3.40.50.10540 CATHdb (see all for 1xvt)
Click To Show Structure

Enzyme Reaction (EC:2.8.3.21)

(R)-carnitine
CHEBI:16347ChEBI
+
gamma-butyrobetainyl-CoA(3-)
CHEBI:61513ChEBI
→
(R)-carnitinyl-CoA(3-)
CHEBI:60932ChEBI
+
4-(trimethylammonio)butanoate
CHEBI:16244ChEBI
Alternative enzyme names: CaiB, Crotonobetainyl/gamma-butyrobetainyl-CoA:carnitine CoA-transferase,

Enzyme Mechanism

Introduction

By analogy with Formyl-CoA transferase, Asp 169 is nucleophilic and attacks the carbonyl carbon of the crotonobetainyl-CoA thioester group. This displaces the coenzyme A thiolate. CoAS- then displaces the coronobetainyl intermediate on Asp169. Carnitine enters the active site and the carboxylate group is nucleophilic and attacks the gamma-carbon of the Asp 169 side chain which displaces the crotonobetaine product and forms a new anhydride intermediate. The CoA thiolate attacks the carbonyl group of the carnitine moiety, displacing and regenerating Asp 169 and forming the carnitine-CoA product.

Catalytic Residues Roles

UniProt PDB* (1xvt)
Asp169 Asp169(172)A Asp 169 acts as a nucleophilic catalyst. It displaces the CoA thiolate from crotonobetainyl-CoA and remains acylated in the anhydride intermediates. covalently attached, nucleofuge, nucleophile, electrofuge, electrophile
*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

bimolecular nucleophilic substitution, enzyme-substrate complex formation, intermediate formation, intermediate collapse, enzyme-substrate complex cleavage, overall reactant used, native state of enzyme regenerated, overall product formed, intermediate terminated

References

  1. Berthold CL et al. (2008), J Biol Chem, 283, 6519-6529. Reinvestigation of the catalytic mechanism of formyl-CoA transferase, a class III CoA-transferase. DOI:10.1074/jbc.M709353200. PMID:18162462.
  2. Rangarajan ES et al. (2005), Biochemistry, 44, 5728-5738. Crystal Structure ofEscherichia coliCrotonobetainyl-CoA:  Carnitine CoA-Transferase (CaiB) and Its Complexes with CoA and Carnitinyl-CoA†. DOI:10.1021/bi047656f. PMID:15823031.
  3. Jonsson S et al. (2004), J Biol Chem, 279, 36003-36012. Kinetic and Mechanistic Characterization of the Formyl-CoA Transferase from Oxalobacter formigenes. DOI:10.1074/jbc.m404873200. PMID:15213226.

Step 1. Asp169 performs a nucleophilic attack on the carbonyl carbon on crotonobetainyl-CoA.

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Catalytic Residues Roles

Residue Roles
Asp169(172)A covalently attached, nucleophile

Chemical Components

ingold: bimolecular nucleophilic substitution, enzyme-substrate complex formation, intermediate formation

Step 2. Thiolate on CoA is nucleophilic and attacks the Asp169 intermediate, producing the (trimethylammonio)butanoate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp169(172)A covalently attached, electrofuge, electrophile

Chemical Components

ingold: bimolecular nucleophilic substitution, intermediate collapse, enzyme-substrate complex cleavage, enzyme-substrate complex formation

Step 3. Carnitine enters the active site to acts as a nucleophile and attack the aspartyl-CoA thioester to form another enzyme-substrate intermediate.

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Catalytic Residues Roles

Residue Roles
Asp169(172)A covalently attached

Chemical Components

ingold: bimolecular nucleophilic substitution, overall reactant used, enzyme-substrate complex formation, enzyme-substrate complex cleavage, intermediate collapse

Step 4. CoA thiolate then performs a nucleophilic attack on the carbonyl carbon on aspartyl-carnitine.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp169(172)A nucleofuge

Chemical Components

ingold: bimolecular nucleophilic substitution, enzyme-substrate complex cleavage, native state of enzyme regenerated, overall product formed, intermediate terminated
Download: Image, Marvin File

Step 1. Asp169 performs a nucleophilic attack on the carbonyl carbon on crotonobetainyl-CoA.

Step 2. Thiolate on CoA is nucleophilic and attacks the Asp169 intermediate, producing the (trimethylammonio)butanoate.

Step 3. Carnitine enters the active site to acts as a nucleophile and attack the aspartyl-CoA thioester to form another enzyme-substrate intermediate.

Step 4. CoA thiolate then performs a nucleophilic attack on the carbonyl carbon on aspartyl-carnitine.

Products.

Contributors

Jonathan T. W. Ng, Gemma L. Holliday, Morwenna Hall