Cofactors

Iron-sulfur; Thiamine diphosphate.

Reaction Mechanism

pyruvate:ferredoxin oxidoreducatse By Reference

Pyruvate:ferrodoxin/flavodoxin reductases (PFORs) catalyse the oxidative decarboxylation of pyruvate to acetyl-CoA in anaerobic organisms. PFORs can occur in both obligately and facultatively anaerobic bacteria and also some eukaryotic microorganisms. PFORs are single-chain enzymes containing a thiamin pyrophosphate cofactor for the cleavage of carbon-carbon bonds next to a carbonyl group, and iron-sulphur clusters for electron transfer. Ferredoxin I and ferredoxin II, which are single 4Fe-4S cluster ferredoxins are the most effective electron carriers for PFORs in Desulfovibrio africanus.




• Summary
• Step 1
• Step 2
• Step 3
• Step 4
• Step 5
• Step 6
• Step 7
• Products

The catalytic mechanism of PDC for the most part follows the principles of catalytic mechanisms of other TPP-dependent enzymes: carbonyl addition of pyruvate to the reactive C2 atom of the cofactor thiazolium ring yields the intermediate 2-(2-lactyl)-TDP (LTDP). The subsequent release of carbon dioxide produces resonating carbanion/enamine forms of 2-(1-hydroxyethyl)-TDP (HETDP, also known as hydroxyethylidene-TPP). The resonating form is considered to be a central and highly reactive intermediate state in TPP-dependent enzymes acting on pyruvate. However, unlike most other TPP-dependent enzymes in which the intermediate is oxidized, the carbanion/enamine in PDC is protonated at the C2α position, yielding C2alpha-hydroxylethylthiamine diphosphate (HETDP) before the final release of acetaldehyde completes the reaction.

Catalytic Residues

AA	Uniprot	Uniprot Resid	PDB	PDB Resid
Asn	P94692	996	2c3m	995
Thr	P94692	31	2c3m	30
Glu	P94692	64	2c3m	63
Arg	P94692	114	2c3m	113

Step Components

overall product formed, proton transfer, assisted tautomerisation (not keto-enol), native state of cofactor regenerated, intermediate formation, colligation, electron relay, cofactor used, redox reaction, homolysis, intermediate terminated, native state of enzyme regenerated, decarboxylation, intermediate collapse, radical formation, hydride transfer, overall reactant used, inferred reaction step, unimolecular elimination by the conjugate base, bimolecular nucleophilic addition, tautomerisation (not keto-enol)



Step 1.

Glu64 deprotonates the thiamine diphosphate cofactor, which initiates double bond rearrangement that results in the deprotonation of the N=CH-S group, activating the cofactor.

The cofactor adopts the V configuration that brings the 4 imino group of the aminopyrimidine ring close to the C2 carbon of the thiazolium ring [PMID:16472741]. Hydrogen bonding of the carboxylate group from Glu64 to N1' of the aminopyrimidine ring increases the basic nature of the 4' position by generating the 4'-imino tautomer [PMID:11752578]. Binding of the substrate triggers the proton transfers [PMID10048931]. The mechanism shown here is supported by crystallographic studies [PMID:16472741].



Step 2.

The carbanion of thiamine diphosphate initiates a nucleophilic attack on the carbonyl carbon of pyruvate in an addition reaction that results in the cofactor undergoing double bond rearrangement that results in the deprotonation of Glu64.



Step 3.

The covalently bound pyruvate undergoes decarboxylation, resulting in double bond rearrangement, a single electron being transferred to ferredoxin via three iron-sulfur clusters and the formation of a one-electron bond between the cofactor and the formyl group.

The carbon dioxide reaction product remains tightly bound in the active site, consistent with the reversibility of the reaction [PMID:16472741]. The C2alpha-C2 bond between the acetyl and thiazole moieties is a one-electron unusually long bond PMID:11752578,PMID:16472741] and thus incompatible with enamine formation as postulated for a standard pyruvate decarboxylation cycle [PMID:16472741]. The generated intermediate shown here is supported by crystallographic studies [PMID:16472741].



Step 4.

The C-C one electron bond between the cofator and the formyl group fragments.



Step 5.

Water deprotonates CoA, which initiates a single electron transfer to ferredoxin through three iron-sulfur clusters.



Step 6.

The CoA thiyl and the acetyl radicals undergo colligation.



Step 7.

The cofactor is regenerated through the nitrogen donating its lone pair into the ring to satisfy the electron deficient carbon.



Products.

The products of the reaction.

View Reaction Mechanisms in M-CSA

Reaction Parameters

There are no kinetic parameters information for this Enzyme

Associated Proteins

Citations

• New light on ancient enzymes - in vitro CO₂ Fixation by Pyruvate Synthase of Desulfovibrio africanus and Sulfolobus acidocaldarius.
• Succinylation modification: a potential therapeutic target in stroke.
• Evaluation of Cell Responses of Saccharomyces cerevisiae under Cultivation Using Wheat Bran as a Nutrient Resource by Analyses of Growth Activities and Comprehensive Gene Transcription Levels
• Changes in Plasma Pyruvate and TCA Cycle Metabolites upon Increased Hepatic Fatty Acid Oxidation and Ketogenesis in Male Wistar Rats.
• Metabolic adaptation and ATP homeostasis in Pseudomonas fluorescens exposed to phosphate stress
• Meta-analysis of transcriptome reveals key genes relating to oil quality in olive.
• Osthole inhibits GSK-3β/AMPK/mTOR pathway-controlled glycolysis and increases radiosensitivity of subcutaneous transplanted hepatocellular carcinoma in nude mice.
• Wheat germ peptide improves glucose metabolism and insulin resistance in HepG2 hepatocytes via regulating SOCS3/IRS1/Akt pathway.
• IAR4 mutation enhances cadmium toxicity by disturbing auxin homeostasis in Arabidopsis thaliana.
• (R/S)-lactate/2-hydroxybutyrate dehydrogenases in and biosynthesis of block copolyesters by Ralstonia eutropha.
• The interdependence of isoprenoid synthesis and apicoplast biogenesis in malaria parasites.