Holo-[acyl-carrier-protein] synthase

 

Holo-(acyl carrier protein) synthase (AcpS) from Bacillus subtilis is a member of the phosphopantetheinyl transferase superfamily. AcpS post-translationally modifies ACP to its holo form in order to activate it. AcpS catalyses the transfer of the 4'-phosphopantetheinyl (P-pant) moiety of coenzyme A to a serine residue on the ACP. This gives the activated ACP enzyme and Adenosine 3'5'-bisphosphate as products. This process is important as ACP enzymes play important roles in a number of biosynthetic pathways, such as the synthesis of fatty acids, vitamins, AcpS is essential in the initiation of the biosynthesis of fatty acids, polyketide antibiotics and non-ribosomal peptides.

 

Reference Protein and Structure

Sequences
P96618 UniProt (2.7.8.7)
P80643 UniProt IPR002582 (Sequence Homologues) (PDB Homologues)
Biological species
Bacillus subtilis subsp. subtilis str. 168 (Bacteria) Uniprot
PDB
1f80 - HOLO-(ACYL CARRIER PROTEIN) SYNTHASE IN COMPLEX WITH HOLO-(ACYL CARRIER PROTEIN) (2.3 Å) PDBe PDBsum 1f80
Catalytic CATH Domains
3.90.470.20 CATHdb 1.10.1200.10 CATHdb (see all for 1f80)
Cofactors
Calcium(2+) (1), Magnesium(2+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:2.7.8.7)

coenzyme A(4-)
CHEBI:57287ChEBI
+
L-serine residue
CHEBI:29999ChEBI
→
O-(pantetheine-4'-phosphoryl)serine(1-) residue
CHEBI:64479ChEBI
+
adenosine 3',5'-bismonophosphate(4-)
CHEBI:58343ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: Acyl carrier protein holoprotein (holo-ACP) synthetase, Acyl carrier protein synthetase, Coenzyme A:fatty acid synthetase apoenzyme 4'-phosphopantetheine transferase, Holo-ACP synthase, Holo-ACP synthetase, Holosynthase, PPTase, AcpS, ACPS, Acyl carrier protein synthase, P-pant transferase, CoA:apo-[acyl-carrier-protein] pantetheinephosphotransferase, L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase, 4'-phosphopantetheinyl transferase, Alpha-aminoadipic semialdehyde dehydrogenase-phosphopantetheinyl transferase,

Enzyme Mechanism

Introduction

This enzyme requires either Mg(II) or Mn(II) for activity. The mechanism proceeds as follows: Asp 35 (in the substrate protein) deprotonates a water molecule. This activated water molecule then acts as a general base by deprotonating the substrate serine residue, activating it for nucleophilic attack on the beta-phosphate of CoA. The nucleophilic attack results in the transfer of the phosphopantetheinyl group to the substrate serine residue. The resulting negatively charged 3',5'-ADP is stabilised by interactions with Lys 62, the mainchain amide of His 105 and the magnesium ion. A proton is then transferred to 3',5'-ADP from either a water molecule or Lys 62.

Catalytic Residues Roles

UniProt PDB* (1f80)
His105 (main-N) His105(104)B (main-N) The main-chain amide of His 105 stabilises the negatively charged 3',5'-ADP. electrostatic stabiliser
Lys62 Lys62(61)A Stabilises the negatively charged intermediate. May also act as a proton donor to 3',5'-ADP. electrostatic stabiliser
Asp36 Asp35(40)E This residue is part of the substrate protein (represented by UniProtKB P80643). It deprotonates a water molecule, which in turn deprotonates the substrate serine residue. proton acceptor
*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 relay, intermediate formation, overall reactant used, proton transfer, bimolecular nucleophilic addition, overall product formed, intermediate terminated, intermediate collapse, unimolecular elimination by the conjugate base

References

  1. Parris KD et al. (2000), Structure, 8, 883-895. Crystal structures of substrate binding to Bacillus subtilis holo-(acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites. DOI:10.1016/s0969-2126(00)00178-7. PMID:10997907.

Step 1. Magnesium activated water deprotonates the Apo-ACP, activating it.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys62(61)A electrostatic stabiliser
His105(104)B (main-N) electrostatic stabiliser
Asp35(40)E proton acceptor

Chemical Components

proton relay, intermediate formation, overall reactant used, proton transfer

Step 2. The activated Apo-ACP attacks the CoA in a nucleophilic addition, creating a pentavalent phosphate intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys62(61)A electrostatic stabiliser
His105(104)B (main-N) electrostatic stabiliser

Chemical Components

intermediate formation, overall reactant used, ingold: bimolecular nucleophilic addition

Step 3. The pentavalent phosphate intermediate collapses, initiating an elimination of the adenosine 3',5'-bisphosphate product, which is reprotonated from a water molecule.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys62(61)A electrostatic stabiliser
His105(104)B (main-N) electrostatic stabiliser

Chemical Components

overall product formed, intermediate terminated, intermediate collapse, proton transfer, ingold: unimolecular elimination by the conjugate base
Download: Image, Marvin File

Step 1. Magnesium activated water deprotonates the Apo-ACP, activating it.

Step 2. The activated Apo-ACP attacks the CoA in a nucleophilic addition, creating a pentavalent phosphate intermediate.

Step 3. The pentavalent phosphate intermediate collapses, initiating an elimination of the adenosine 3',5'-bisphosphate product, which is reprotonated from a water molecule.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid