Acyl-[acyl-carrier-protein] desaturase

 

Delta-9 stearoyl-acyl carrier protein desaturase (delta-9 desaturase) is a plastid-localised non-membrane-bound soluble desaturase that introduces the first double bond into saturated fatty acids, resulting in the corresponding mono-unsaturated fatty acids.

 

Reference Protein and Structure

Sequence
P22337 UniProt (1.14.19.2) IPR005067 (Sequence Homologues) (PDB Homologues)
Biological species
Ricinus communis (castor bean) Uniprot
PDB
1afr - STEAROYL-ACYL CARRIER PROTEIN DESATURASE FROM CASTOR SEEDS (2.4 Å) PDBe PDBsum 1afr
Catalytic CATH Domains
1.10.620.20 CATHdb (see all for 1afr)
Cofactors
Iron(2+) (2) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:1.14.19.2)

O-(S-octadecanoylpantetheine-4'-phosphoryl)serine(1-) residue
CHEBI:78495ChEBI
+
hydron
CHEBI:15378ChEBI
+
dioxygen
CHEBI:15379ChEBI
+
di-mu-sulfido-diiron(1+)
CHEBI:33738ChEBI
→
water
CHEBI:15377ChEBI
+
O-(S-oleoylpantetheine-4'-phosphoryl)serine(1-) residue
CHEBI:78783ChEBI
+
di-mu-sulfido-diiron(2+)
CHEBI:33737ChEBI
Alternative enzyme names: Stearyl acyl carrier protein desaturase, Stearyl-ACP desaturase, Acyl-[acyl-carrier-protein] desaturase, Acyl-[acyl-carrier protein],hydrogen-donor:oxygen oxidoreductase,

Enzyme Mechanism

Introduction

An electron transport chain carries an electron from ferredoxin to one of the iron centres via several residues. A second electron is then carried to the second iron centre. Several redox reactions take place involving oxygen, water and the iron centres, which result in deprotonation of the substrate and formation of a double bond.

There are two possible paths for the electron transport chain - the one described here has been chosen because of its analogy to what has been suggested for E. coli ribonucleotide reductase protein R2.

Catalytic Residues Roles

UniProt PDB* (1afr)
Trp95 Trp62(44)A Transfers electron from ferredoxin to Asp228. single electron relay, single electron acceptor, single electron donor, hydrogen bond donor
His179 His146(128)A Transfers electron from Asp228 to Fe365 in the first step and to Fe364 in the second step. single electron relay, hydrogen bond donor, metal ligand, single electron acceptor, single electron donor
Thr232 Thr199(181)A Helps stabilise the active dioxo intermediate. hydrogen bond donor, electrostatic stabiliser
Asp261 Asp228(210)A Transfers electron from Trp62 to His146. single electron relay, single electron donor, single electron acceptor, hydrogen bond acceptor
Glu229, His265 Glu196(178)A, His232(214)A Forms part of the Iron 2 binding site. metal ligand
Glu138 Glu105(87)A Forms part of Iron 1 binding site. metal ligand
Glu262, Glu176 Glu229(211)A, Glu143(125)A Act as bridging ligands between the two iron centres. 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

electron transfer, overall reactant used, cofactor used, intermediate formation, electron relay, elimination (not covered by the Ingold mechanisms), heterolysis, decoordination from a metal ion, bimolecular homolytic addition, coordination, coordination to a metal ion, proton transfer, colligation, hydrogen transfer, bimolecular elimination, hydride transfer, bimolecular nucleophilic substitution, native state of cofactor regenerated, intermediate terminated, intermediate collapse, overall product formed, native state of enzyme regenerated

References

  1. Lindqvist Y et al. (1996), EMBO J, 15, 4081-4092. Crystal structure of delta9 stearoyl-acyl carrier protein desaturase from castor seed and its relationship to other di-iron proteins. PMID:8861937.
  2. Liu Q et al. (2015), Plant Physiol, 169, 432-441. Half-of-the-Sites Reactivity of the Castor Δ9-18:0-Acyl Carrier Protein Desaturase. DOI:10.1104/pp.15.00622. PMID:26224800.
  3. Guy JE et al. (2011), Proc Natl Acad Sci U S A, 108, 16594-16599. Remote control of regioselectivity in acyl-acyl carrier protein-desaturases. DOI:10.1073/pnas.1110221108. PMID:21930947.
  4. Guy JE et al. (2006), Proc Natl Acad Sci U S A, 103, 17220-17224. A single mutation in the castor Delta9-18:0-desaturase changes reaction partitioning from desaturation to oxidase chemistry. DOI:10.1073/pnas.0607165103. PMID:17088542.
  5. Fox BG et al. (2004), Acc Chem Res, 37, 421-429. Reactions of the Diiron Enzyme Stearoyl-Acyl Carrier Protein Desaturase. DOI:10.1021/ar030186h. PMID:15260504.
  6. Moche M et al. (2003), J Biol Chem, 278, 25072-25080. Azide and acetate complexes plus two iron-depleted crystal structures of the di-iron enzyme delta9 stearoyl-acyl carrier protein desaturase. Implications for oxygen activation and catalytic intermediates. DOI:10.1074/jbc.M301662200. PMID:12704186.
  7. Nordlund P et al. (1993), J Mol Biol, 232, 123-164. Structure and Function of the Escherichia coli Ribonucleotide Reductase Protein R2. DOI:10.1006/jmbi.1993.1374. PMID:8331655.

Step 1. Ferredoxin donates a single electron, through Trp62, Asp228 and His146, to one of the Fe(III) centres.

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Catalytic Residues Roles

Residue Roles
Trp62(44)A hydrogen bond donor
His146(128)A hydrogen bond donor
Asp228(210)A hydrogen bond acceptor
Glu105(87)A metal ligand
Glu229(211)A metal ligand
Glu143(125)A metal ligand
His146(128)A metal ligand
Glu196(178)A metal ligand
His232(214)A metal ligand
Trp62(44)A single electron relay
His146(128)A single electron relay
Asp228(210)A single electron relay
His146(128)A single electron acceptor
Asp228(210)A single electron donor
His146(128)A single electron donor
Trp62(44)A single electron acceptor, single electron donor
Asp228(210)A single electron acceptor

Chemical Components

electron transfer, overall reactant used, cofactor used, intermediate formation, electron relay

Step 2. Ferredoxin donates a second single electron, through Trp62, Asp228 and His146, to the second Fe(III) centre, which initiates the loss of the bridging O2- ion. This oxygen atom is displaced by dioxygen.

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Catalytic Residues Roles

Residue Roles
Trp62(44)A hydrogen bond donor
His146(128)A hydrogen bond donor
Asp228(210)A hydrogen bond acceptor
Glu105(87)A metal ligand
Glu229(211)A metal ligand
Glu143(125)A metal ligand
His146(128)A metal ligand
Glu196(178)A metal ligand
His232(214)A metal ligand
Trp62(44)A single electron relay
His146(128)A single electron relay
Asp228(210)A single electron relay, single electron acceptor
His146(128)A single electron donor
Asp228(210)A single electron donor
His146(128)A single electron acceptor
Trp62(44)A single electron acceptor, single electron donor

Chemical Components

electron transfer, elimination (not covered by the Ingold mechanisms), heterolysis, overall reactant used, cofactor used, intermediate formation, electron relay, decoordination from a metal ion

Step 3. Water coordinates to one of the Fe(II) centres, which causes the centre to donate a single electron to the dioxide molecule, initiating the first of two homolytic additions of the dioxygen molecule to both Fe(II) centres and the second Fe(II) centre also donates a single electron to the dioxygen bridge.

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Catalytic Residues Roles

Residue Roles
Trp62(44)A hydrogen bond donor
His146(128)A hydrogen bond donor
Thr199(181)A hydrogen bond donor, electrostatic stabiliser
Asp228(210)A hydrogen bond acceptor
Glu105(87)A metal ligand
Glu229(211)A metal ligand
Glu143(125)A metal ligand
His146(128)A metal ligand
Glu196(178)A metal ligand
His232(214)A metal ligand

Chemical Components

ingold: bimolecular homolytic addition, coordination, coordination to a metal ion, intermediate formation

Step 4. Both Fe(III) centres donate a single electron to the bridging dioxygen, cleaving the O-O bond and initiating one of the oxygen atoms to deprotonates the bound water and regenerating the oxo-bridge.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Trp62(44)A hydrogen bond donor
His146(128)A hydrogen bond donor
Thr199(181)A hydrogen bond donor
Asp228(210)A hydrogen bond acceptor
Thr199(181)A electrostatic stabiliser
Glu105(87)A metal ligand
Glu229(211)A metal ligand
Glu143(125)A metal ligand
His146(128)A metal ligand
Glu196(178)A metal ligand
His232(214)A metal ligand

Chemical Components

electron transfer, elimination (not covered by the Ingold mechanisms), proton transfer, colligation, hydrogen transfer, coordination to a metal ion, intermediate formation

Step 5. The hydroxide on the first Fe(IV) centre deprotonates the stearoyl-[acyl-carrier protein] substrate, initiating the elimination of a hydride ion, which attacks the second Fe(IV) bound hydroxide. The excess electrons are donated singly to both Fe(IV) centres, regenerating the enzyme.

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Catalytic Residues Roles

Residue Roles
Trp62(44)A hydrogen bond donor
His146(128)A hydrogen bond donor
Asp228(210)A hydrogen bond acceptor
Glu105(87)A metal ligand
Glu229(211)A metal ligand
Glu143(125)A metal ligand
His146(128)A metal ligand
Glu196(178)A metal ligand
His232(214)A metal ligand

Chemical Components

ingold: bimolecular elimination, hydride transfer, ingold: bimolecular nucleophilic substitution, electron transfer, elimination (not covered by the Ingold mechanisms), overall reactant used, native state of cofactor regenerated, decoordination from a metal ion, intermediate terminated, intermediate collapse, overall product formed, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Ferredoxin donates a single electron, through Trp62, Asp228 and His146, to one of the Fe(III) centres.

Step 2. Ferredoxin donates a second single electron, through Trp62, Asp228 and His146, to the second Fe(III) centre, which initiates the loss of the bridging O2- ion. This oxygen atom is displaced by dioxygen.

Step 3. Water coordinates to one of the Fe(II) centres, which causes the centre to donate a single electron to the dioxide molecule, initiating the first of two homolytic additions of the dioxygen molecule to both Fe(II) centres and the second Fe(II) centre also donates a single electron to the dioxygen bridge.

Step 4. Both Fe(III) centres donate a single electron to the bridging dioxygen, cleaving the O-O bond and initiating one of the oxygen atoms to deprotonates the bound water and regenerating the oxo-bridge.

Step 5. The hydroxide on the first Fe(IV) centre deprotonates the stearoyl-[acyl-carrier protein] substrate, initiating the elimination of a hydride ion, which attacks the second Fe(IV) bound hydroxide. The excess electrons are donated singly to both Fe(IV) centres, regenerating the enzyme.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, James W. Murray, Craig Porter