Long-chain-fatty-acid-CoA ligase

 

Long chain fatty acid coenzyme-A synthetase (LC-FACS) participates in the first reaction step of long chain fatty acid degradation. These enzymes act on a wide range of long-chain saturated and unsaturated fatty acids, but the enzymes from different tissues and species show some variation in specificity. For example, the liver enzyme acts on acids from C6 to C20, that from brain shows high activity up to C24, and the enzyme from Thermus thermophilus acts on C12 to C22 fatty acids. LC-FACS catalyses the conversion of long chain fatty acids into fatty-acyl-CoA, creating AMP and pyrophosphate as bi-products. LC-FACS is responsible for physiological regulation of cellular functions, as well as fatty acid degradation.

 

Reference Protein and Structure

Sequence
Q5SKN9 UniProt (6.2.1.3) IPR000873 (Sequence Homologues) (PDB Homologues)
Biological species
Thermus thermophilus HB8 (Bacteria) Uniprot
PDB
1v25 - Crystal structure of tt0168 from Thermus thermophilus HB8 (2.3 Å) PDBe PDBsum 1v25
Catalytic CATH Domains
3.40.50.12780 CATHdb 3.30.300.310 CATHdb (see all for 1v25)
Cofactors
Magnesium(2+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:6.2.1.3)

ATP(4-)
CHEBI:30616ChEBI
+
long-chain fatty acid anion
CHEBI:57560ChEBI
+
coenzyme A(4-)
CHEBI:57287ChEBI
→
adenosine 5'-monophosphate(2-)
CHEBI:456215ChEBI
+
long-chain fatty acyl-CoA(4-)
CHEBI:83139ChEBI
+
diphosphate(3-)
CHEBI:33019ChEBI
Alternative enzyme names: ACS3, FAA1, LCFA synthetase, Acyl coenzyme A synthetase, Acyl-CoA ligase, Acyl-CoA synthetase, Acyl-activating enzyme, Acyl-coenzyme A ligase, Arachidonyl-CoA synthetase, Fatty acid CoA ligase, Fatty acid elongase, Fatty acid thiokinase (long chain), Fatty acyl-coenzyme A synthetase, Lignoceroyl-CoA synthase, Long chain fatty acyl-CoA synthetase, Long-chain acyl CoA synthetase, Long-chain acyl-CoA synthetase I, Long-chain acyl-CoA synthetase II, Long-chain acyl-coenzyme A synthetase, Long-chain fatty acyl coenzyme A synthetase, Oleoyl-CoA synthetase, Palmitoyl coenzyme A synthetase, Palmitoyl-CoA ligase, Palmitoyl-CoA synthase, Pristanoyl-CoA synthetase, Stearoyl-CoA synthetase, Thiokinase,

Enzyme Mechanism

Introduction

Trp 444 hydrogen bonds to the alpha-phosphorus atom, making the alpha-phosphorus electron deficient, and a better electrophile. This is helped by the electrostatic interaction of Mg(II). The carbonyl oxygen of the fatty acid nucleophilically attacks the alpha-phosphorus atom, forming a negatively charged, penta-coordinated intermediate. This intermediate is stabilised through interactions between the O1A atom of the substrate and the indole ring of Trp 444. As the intermediate collapses, the scissile P-O bond is broken, resulting in a fatty-acyl-AMP, and a pyrophosphate leaving group.

Lys 439 hydrogen bonds to the carbonyl oxygen atom of the fatty-acyl-AMP, and the O1A atom of the alpha-phosphorus, generating an electron deficient carbonyl carbon, making it more electrophilic. The S atom of CoA nucleophilically attacks the fatty-acyl-AMP carbonyl carbon, breaking the C-O ester bond. This forms the fatty-acyl-CoA product, and a negatively charged AMP, which is stabilised by Lys 439.

Catalytic Residues Roles

UniProt PDB* (1v25)
Trp444 Trp444A Acts to make the alpha-phosphorus atom more electrophilic. stabilises the negatively charged intermediate. hydrogen bond donor, electrostatic stabiliser
Lys439 Lys439A Acts to make the carbonyl carbon atom of fatty-acyl-AMP more electrophilic. Also stabilises the negatively charged AMP leaving group. hydrogen bond donor, electrostatic stabiliser
Thr184, Glu328 Thr184A, Glu328A Forms part of the magnesium binding site. 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

bimolecular nucleophilic addition, unimolecular elimination by the conjugate base, bimolecular nucleophilic substitution, proton transfer

References

  1. Hisanaga Y et al. (2004), J Biol Chem, 279, 31717-31726. Structural Basis of the Substrate-specific Two-step Catalysis of Long Chain Fatty Acyl-CoA Synthetase Dimer. DOI:10.1074/jbc.m400100200. PMID:15145952.
  2. Soupene E et al. (2008), Exp Biol Med (Maywood), 233, 507-521. Mammalian Long-Chain Acyl-CoA Synthetases. DOI:10.3181/0710-mr-287. PMID:18375835.

Step 1. The carboxylate of the long chain carboxylate acts as a nucleophile and attacks the alpha-phosphate of ATP in an addition reaction to form a pentavalent phosphate intermediate. Mg(II), Trp444 and Lys439 stabilise the intermediates formed.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys439A hydrogen bond donor, electrostatic stabiliser
Trp444A hydrogen bond donor, electrostatic stabiliser
Glu328A metal ligand
Thr184A metal ligand

Chemical Components

ingold: bimolecular nucleophilic addition

Step 2. The pentavalent phosphate intermediate breaks down in a conjugate base elimination, liberating pyrophosphate. Mg(II), Trp444 and Lys439 stabilise the intermediates formed.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys439A hydrogen bond donor, electrostatic stabiliser
Trp444A hydrogen bond donor, electrostatic stabiliser
Glu328A metal ligand
Thr184A metal ligand

Chemical Components

ingold: unimolecular elimination by the conjugate base

Step 3. CoA (probably activated by the phosphate group) acts as a nucleophile which attacks the carbonyl group of the intermediate complex in a substitution reaction, liberating AMP. Mg(II), Trp444 and Lys439 stabilise the intermediates formed.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys439A hydrogen bond donor, electrostatic stabiliser
Trp444A hydrogen bond donor, electrostatic stabiliser
Glu328A metal ligand
Thr184A metal ligand

Chemical Components

ingold: bimolecular nucleophilic substitution, proton transfer
Download: Image, Marvin File

Step 1. The carboxylate of the long chain carboxylate acts as a nucleophile and attacks the alpha-phosphate of ATP in an addition reaction to form a pentavalent phosphate intermediate. Mg(II), Trp444 and Lys439 stabilise the intermediates formed.

Step 2. The pentavalent phosphate intermediate breaks down in a conjugate base elimination, liberating pyrophosphate. Mg(II), Trp444 and Lys439 stabilise the intermediates formed.

Step 3. CoA (probably activated by the phosphate group) acts as a nucleophile which attacks the carbonyl group of the intermediate complex in a substitution reaction, liberating AMP. Mg(II), Trp444 and Lys439 stabilise the intermediates formed.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Ellie Wright