Phosphopantothenoylcysteine decarboxylase

 

The Arabidopsis thaliana flavoprotein AtHAL3a catalyses the oxidative decarboxylation of 4'-phosphopantothenoylcysteine to 4'-phosphopantetheine, a step in coenzyme A biosynthesis. It belongs to the family of homo-oligomeric flavin-containing cysteine decarboxylases (HFCD) family.

 

Reference Protein and Structure

Sequence
Q9SWE5 UniProt (4.1.1.36) IPR003382 (Sequence Homologues) (PDB Homologues)
Biological species
Arabidopsis thaliana (Thale cress) Uniprot
PDB
1mvn - PPC decarboxylase mutant C175S complexed with pantothenoylaminoethenethiol (2.21 Å) PDBe PDBsum 1mvn
Catalytic CATH Domains
3.40.50.1950 CATHdb (see all for 1mvn)
Cofactors
Fmnh2(2-) (1)
Click To Show Structure

Enzyme Reaction (EC:4.1.1.36)

N-[(R)-4-phosphonatopantothenoyl]-L-cysteinate(3-)
CHEBI:59458ChEBI
+
hydron
CHEBI:15378ChEBI
→
carbon dioxide
CHEBI:16526ChEBI
+
D-pantetheine 4'-phosphate(2-)
CHEBI:61723ChEBI
Alternative enzyme names: 4-phosphopantothenoyl-L-cysteine decarboxylase, 4-phosphopantotheoylcysteine decarboxylase, PPC-decarboxylase, N-((R)-4'-phosphopantothenoyl)-L-cysteine carboxy-lyase,

Enzyme Mechanism

Introduction

The mechanism involves 2 reaction steps:oxidative decarboxylation to form a thioaldehyde intermediate and the reduction of the intermediate. First, a thiolate ion is stabilised by His90, which acts as a base to deprotonate the thio-group of the substrate cysteine. Electrons are transferred by an SET mechanism from the thiolate to FMN together with the deprotonation of the beta-carbon of the substrate cysteine by His90. This results in a thioaldehyde intermediate which decarboxylates spontaneously, forming a cis ene-thiolate. The ene-thiolate is then reduced by direct hydride transfer from FMNH2 to the beta-carbon atom and the concomitant protonation of the alpha-carbon by Cys175.

Catalytic Residues Roles

UniProt PDB* (1mvn)
Cys175 Ser175A It acts as an acid to deprotonate the alpha-carbon atom in the cis ene-thiolate intermediate, concomitant to the hydride transfer from FMNH2 to the beta-carbon atom, in the reduction of the intermediate. proton donor
His90 His90A(AA) It acts as a base to deprotonate the thio-group of the substrate cysteine to form a thiolate ion. proton acceptor, 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

bimolecular nucleophilic addition, cofactor used, overall reactant used, bimolecular elimination, proton transfer, decarboxylation, overall product formed, hydride transfer, native state of cofactor regenerated, bimolecular electrophilic addition

References

  1. Steinbacher S et al. (2003), J Mol Biol, 327, 193-202. Crystal Structure of the Plant PPC Decarboxylase AtHAL3a Complexed with an Ene-thiol Reaction Intermediate. DOI:10.1016/s0022-2836(03)00092-5. PMID:12614618.
  2. Strauss E et al. (2004), Biochemistry, 43, 15520-15533. Mechanistic studies on phosphopantothenoylcysteine decarboxylase: trapping of an enethiolate intermediate with a mechanism-based inactivating agent. DOI:10.1021/bi048340a. PMID:15581364.
  3. Kupke T et al. (2001), J Biol Chem, 276, 19190-19196. Arabidopsis thaliana Flavoprotein AtHAL3a Catalyzes the Decarboxylation of 4'-Phosphopantothenoylcysteine to 4'-Phosphopantetheine, a Key Step in Coenzyme A Biosynthesis. DOI:10.1074/jbc.m100776200. PMID:11279129.
  4. Andersson I (1996), J Mol Biol, 259, 160-174. Large Structures at High Resolution: The 1.6 Å Crystal Structure of Spinach Ribulose-1,5- Bisphosphate Carboxylase/Oxygenase Complexed with 2-Carboxyarabinitol Bisphosphate. DOI:10.1006/jmbi.1996.0310. PMID:8648644.
  5. Newman J et al. (1994), Structure, 2, 495-502. Structure of an effector-induced inactivated state of ribulose 1,5-bisphosphate carboxylase/oxygenase: the binary complex between enzyme and xylulose 1,5-bisphosphate. DOI:10.1016/s0969-2126(00)00050-2. PMID:7922027.
  6. Newman J et al. (1993), J Biol Chem, 268, 25876-25886. The X-ray structure of Synechococcus ribulose-bisphosphate carboxylase/oxygenase-activated quaternary complex at 2.2-A resolution. PMID:8245022.

Step 1. The thiolate performs a nucleophilic attack onto the FMN cofactor. His90 acts to stabilize the thiolate.

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Catalytic Residues Roles

Residue Roles
His90A(AA) electrostatic stabiliser

Chemical Components

ingold: bimolecular nucleophilic addition, cofactor used, overall reactant used

Step 2. His90 acts as a base deprotonating the beta carbon of the reactant. This leads to the formation of a thioaldehyde.

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Catalytic Residues Roles

Residue Roles
His90A(AA) electrostatic stabiliser
His90A(AA) proton acceptor

Chemical Components

ingold: bimolecular elimination, proton transfer

Step 3. The thioaldehyde is then spontaneously decarboxylated forming a cis-ene-thiolate.

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Catalytic Residues Roles

Residue Roles

Chemical Components

decarboxylation

Step 4. Hydride transfer from FMNH2 to the beta-carbon and the concomitant protonation of the alpha-carbon by Cys175 leads to the formation of the final product.

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Catalytic Residues Roles

Residue Roles
Ser175A proton donor

Chemical Components

overall product formed, hydride transfer, proton transfer, native state of cofactor regenerated, ingold: bimolecular electrophilic addition
Download: Image, Marvin File

Step 1. The thiolate performs a nucleophilic attack onto the FMN cofactor. His90 acts to stabilize the thiolate.

Step 2. His90 acts as a base deprotonating the beta carbon of the reactant. This leads to the formation of a thioaldehyde.

Step 3. The thioaldehyde is then spontaneously decarboxylated forming a cis-ene-thiolate.

Step 4. Hydride transfer from FMNH2 to the beta-carbon and the concomitant protonation of the alpha-carbon by Cys175 leads to the formation of the final product.

Products.

Contributors

Mei Leung, Gemma L. Holliday, James Willey