M-CSA Mechanism and Catalytic Site Atlas

3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

The mammalian fatty acid synthase (mFAS) is a multidomain protein with seven different active sites working together for the de novo synthesis of lipids, specifically palmitic acid. The dehydratase (DH) domain of mFAS catalyses the dehydration of the β-hydroxyacyl (HAC) to an α,β-unsaturated acyl intermediate.

Reference Protein and Structure

Sequence: A5YV76 (Sequence Homologues) (PDB Homologues)
Biological species: Sus scrofa (pig)
PDB: 2vz9 - Crystal Structure of Mammalian Fatty Acid Synthase in complex with NADP (3.3 Å)
Catalytic CATH Domains: 3.10.129.110 (see all for 2vz9)

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Enzyme Reaction (EC:4.2.1.59)

O-[S-(3R)-3-hydroxyacylpantetheine-4'-phosphoryl]serine(1-) residue

CHEBI:78827

→

O-[S-(2E)-2-enoylpantetheine-4'-phosphoryl]-L-serine(1-) residue

CHEBI:78784

water

CHEBI:15377

Enzyme reaction links: IntEnz ENZYME ExplorEnz

Alternative enzyme names: FabZ (gene name), FabA (gene name), D-3-hydroxyoctanoyl-[acyl carrier protein] dehydratase, Beta-hydroxyoctanoyl-acyl carrier protein dehydrase, Beta-hydroxyoctanoyl thioester dehydratase, Beta-hydroxyoctanoyl-ACP-dehydrase, (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] hydro-lyase, (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] hydro-lyase (oct-2-enoyl-[acyl-carrier protein]-forming), 3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase,

Enzyme Mechanism

Mechanism Proposal 1 ☆☆☆

Summary
Step 1
Step 2
Products
All Steps

Introduction

An oxyanion hole formed by an internal hydrogen bond with the β-hydroxyl of the substrate and with the Gly888-amide allows for the deprotonation of the α-carbonyl carbon by His878. This reaction creates an intermediate tautomer that collapses the oxyanion hole and eliminates its hydroxyl group as water by the deprotonation of Asp1033.

Catalytic Residues Roles

UniProt	PDB* (2vz9)
His1037	His1037A	Stabilises the deprotonation of Asp1033.	hydrogen bond donor, electrostatic stabiliser
Tyr1003	Tyr1003A	Stabilises the deprotonation of Asp1033. Inferred by the curator.	hydrogen bond donor, electrostatic stabiliser
Leu885 (main-C)	Leu885A (main-C)	Stabilises His878 by acting as a hydrogen bond acceptor.	hydrogen bond acceptor, electrostatic stabiliser
Gly888 (main-N)	Gly888A (main-N)	Together with an internal hydrogen bond, Gly888 forms a oxyanion hole that stabilises the deprotonation by His878.	hydrogen bond donor, electrostatic stabiliser
His878	His878A	Acts as a general base to deprotonate the α-carbonyl carbon and initiate substrate bond rearrangement.	hydrogen bond donor, proton acceptor
Asp1033	Asp1033A	Acts as general acid to protonate the leaving group.	hydrogen bond donor, proton donor

*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, intermediate formation, aromatic unimolecular elimination by the conjugate base, intermediate collapse, dehydration, overall product formed, rate-determining step

References

Medina FE et al. (2018), ACS Catal, 8, 10267-10278. QM/MM Study of the Reaction Mechanism of the Dehydratase Domain from Mammalian Fatty Acid Synthase. DOI:https://doi.org/10.1021/acscatal.8b02616.
Maier T et al. (2008), Science, 321, 1315-1322. The crystal structure of a mammalian fatty acid synthase. DOI:10.1126/science.1161269. PMID:18772430.

Step 1. An oxyanion hole formed by an internal hydrogen bond with the β-hydroxyl of the substrate and with the Gly888-amide allows for the deprotonation of the α-carbonyl carbon by His878.

Download: Image, Marvin File

Catalytic Residues Roles

Residue	Roles
His878A	hydrogen bond donor
Gly888A (main-N)	electrostatic stabiliser
Leu885A (main-C)	electrostatic stabiliser
His1037A	electrostatic stabiliser
Tyr1003A	electrostatic stabiliser
His878A	proton acceptor
Leu885A (main-C)	hydrogen bond acceptor
Gly888A (main-N)	hydrogen bond donor
Asp1033A	hydrogen bond donor
Tyr1003A	hydrogen bond donor
His1037A	hydrogen bond donor

Chemical Components

proton transfer, intermediate formation

Step 2. The oxyanion hole collapses, initiating double bond rearrangement. Asp1033 is deprotonated by the hydroxyl group producing water as a leaving group.

Download: Image, Marvin File

Catalytic Residues Roles

Residue	Roles
Gly888A (main-N)	electrostatic stabiliser
Asp1033A	proton donor
His1037A	electrostatic stabiliser, hydrogen bond donor
Tyr1003A	hydrogen bond donor, electrostatic stabiliser
Leu885A (main-C)	hydrogen bond acceptor, electrostatic stabiliser

Chemical Components

proton transfer, ingold: aromatic unimolecular elimination by the conjugate base, intermediate collapse, dehydration, overall product formed, rate-determining step

Download: Image, Marvin File

Step 1. An oxyanion hole formed by an internal hydrogen bond with the β-hydroxyl of the substrate and with the Gly888-amide allows for the deprotonation of the α-carbonyl carbon by His878.

Step 2. The oxyanion hole collapses, initiating double bond rearrangement. Asp1033 is deprotonated by the hydroxyl group producing water as a leaving group.

Products.

Contributors

Marko Babić, Noa Marson