Fatty acid synthase - β-ketoreductase (KR)

 

Fatty acid synthase is a multi-enzyme (i.e. enzyme with multiple catalytic domains) involved in the synthesis of palmitic acid from acetyl-CoA, malonyl-CoA, and NADPH. β-ketoreductase (KR) is one catalytic domain of fatty acid synthetase responsible for reduction of β-ketoacyl moiety of the substrate to β-hydroxyacyl by a NADPH cofactor. Structure alignments of the KR domains have revealed that the main residues that interact with the β-ketoacyl substrate and the nicotinamide ring of the NADPH cofactor are similarly placed and are the same for the different organisms.

 

Reference Protein and Structure

Sequence
P49327 UniProt (1.1.1.100, 1.3.1.39, 2.3.1.38, 2.3.1.39, 2.3.1.41, 2.3.1.85, 3.1.2.14, 4.2.1.59) IPR013968 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
4piv - Human Fatty Acid Synthase Psi/KR Tri-Domain with NADPH and GSK2194069 (2.299 Å) PDBe PDBsum 4piv
Catalytic CATH Domains
3.40.50.720 CATHdb (see all for 4piv)
Click To Show Structure

Enzyme Reaction (EC:2.3.1.85)

O-(S-3-oxoacylpantetheine-4'-phosphoryl)-L-serine(1-) residue
CHEBI:78776ChEBI
+
hydron
CHEBI:15378ChEBI
+
NADPH(4-)
CHEBI:57783ChEBI
→
O-[S-(3R)-3-hydroxyacylpantetheine-4'-phosphoryl]serine(1-) residue
CHEBI:78827ChEBI
+
NADP(3-)
CHEBI:58349ChEBI
Alternative enzyme names: FASN (gene name), Fatty-acid synthase,

Enzyme Mechanism

Introduction

The reaction mechanism of human β-ketoacyl reductase consists of two main stages: (i) a nucleophilic attack of a hydride from NADPH to the β-carbon (Cβ) of the substrate and (ii) β-alkoxide moiety of the substrate deprotonates a nearby Tyr2034, with its protonation restored by a nearby Lys1995, via the ribose’s hydroxyl in NADP+

Catalytic Residues Roles

UniProt PDB* (4piv)
Ser2021 Ser2021(561)A Ser2021 is involved in the formation of an oxyanion hole for the stabilization of Cβ-oxygen of the transition state. electrostatic stabiliser
Tyr2034 Tyr2034(574)A Tyr2034 is involved in the formation of an oxyanion hole for the stabilization of Cβ-oxygen of the transition state. Tyr2034 also acts as a general acid to donate a proton to the substrate. proton acceptor, electrostatic stabiliser, proton donor
Lys1995 Lys1995(535)A Lys1995 acts as a general acid for the protonation of the alkoxide in the ribose ring of the NADP+ molecule. proton donor
Asn2038 Asn2038(578)A Atomic charge of Asn2038 remains constant along the reaction path, and slight decreases in the last step, probably indicating its role in stabilizing the Lys1995. 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

hydride transfer, overall product formed, proton transfer

References

  1. Medina FE et al. (2016), Phys Chem Chem Phys, 19, 347-355. A QM/MM study of the reaction mechanism of human β-ketoacyl reductase. DOI:10.1039/c6cp07014k. PMID:27905606.
  2. Xie X et al. (2016), Biochemistry, 55, 1179-1186. Epimerase and Reductase Activities of Polyketide Synthase Ketoreductase Domains Utilize the Same Conserved Tyrosine and Serine Residues. DOI:10.1021/acs.biochem.6b00024. PMID:26863427.
  3. Hardwicke MA et al. (2014), Nat Chem Biol, 10, 774-779. A human fatty acid synthase inhibitor binds β-ketoacyl reductase in the keto-substrate site. DOI:10.1038/nchembio.1603. PMID:25086508.

Step 1. Nucleophilic attack of hydride from the hydrogen of the nicotinamide moiety of NADPH on the Cβ of the substrate.

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Catalytic Residues Roles

Residue Roles
Ser2021(561)A electrostatic stabiliser
Tyr2034(574)A electrostatic stabiliser

Chemical Components

hydride transfer

Step 2. Tyr2034 is deprotonated by the negatively charged Cβ–oxygen atom of β-ketoacyl substrate, forming the hydroxyacyl product.

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Catalytic Residues Roles

Residue Roles
Tyr2034(574)A proton donor

Chemical Components

overall product formed, proton transfer

Step 3. Deprotonation of the C2-hydroxyl of ribose by the negatively charged Tyr2034.

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Catalytic Residues Roles

Residue Roles
Tyr2034(574)A proton acceptor

Chemical Components

proton transfer

Step 4. Deprotonation of Lys1995 by the alkoxide in the ribose ring of NADP+

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Catalytic Residues Roles

Residue Roles
Lys1995(535)A proton donor
Asn2038(578)A electrostatic stabiliser

Chemical Components

proton transfer
Download: Image, Marvin File

Step 1. Nucleophilic attack of hydride from the hydrogen of the nicotinamide moiety of NADPH on the Cβ of the substrate.

Step 2. Tyr2034 is deprotonated by the negatively charged Cβ–oxygen atom of β-ketoacyl substrate, forming the hydroxyacyl product.

Step 3. Deprotonation of the C2-hydroxyl of ribose by the negatively charged Tyr2034.

Step 4. Deprotonation of Lys1995 by the alkoxide in the ribose ring of NADP+

Products.

Contributors

Trung Nguyen, Yordanos Abeje, Antonio Ribeiro