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Overview for MACiE Entry M0119

Version history

General Information

EC Number: 1.2.7.1 (A member of the Oxidoreductases, Acting on the aldehyde or oxo group of donors, With an iron-sulfur protein as acceptor)

Enzyme Name: pyruvate:ferredoxin oxidoreducatse

Biological Species: Desulfovibrio africanus (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • P94692 - Pyruvate-flavodoxin oxidoreductase

Representative PDB Code: 2c3m - CRYSTAL STRUCTURE OF PYRUVATE-FERREDOXIN OXIDOREDUCTASEFROM DESULFOVIBRIO AFRICANUS (Resolution = 1.84 Å).

Catalytic CATH Codes:

"Other" CATH Codes:

Display structure information

Overall Reaction:

Image of oxidised ferredoxin

Image of pyruvate

Image of CoA

right arrow

Image of proton

Image of acetyl-CoA

Image of carbon dioxide

Image of reduced ferredoxin (2-)

oxidised ferredoxin
C00139
CHEBI:17908
pyruvate
C00022
CHEBI:15361
CoA
C00010
CHEBI:57287
proton
C00080
CHEBI:24636
acetyl-CoA
C00024
CHEBI:57288
carbon dioxide
C00011
CHEBI:16526
reduced ferredoxin (2-)
C00138
CHEBI:17513

View similar reactions


Stepwise Description of the Reaction

Step 1Glu64 deprotonates the thiamine diphosphate cofactor, which initiates double bond rearrangement that results in the deprotonation of the N=CH-S group, activating the cofactor.
Step 2The 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 3The 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.
Step 4The C-C one electron bond between the cofator and the formyl group fragments.
Step 5Water deprotonates CoA, which initiates a single electron transfer to ferredoxin through three iron-sulfur clusters.
Step 6The CoA thiyl and the acetyl radicals undergo colligation.
Step 7The cofactor is regenerated through the nitrogen donating its lone pair into the ring to satisfy the electron deficient carbon.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Thr 31 A Side Chain
Glu 64 A Side Chain
Arg 114 A Side Chain
Asn 996 A Side Chain

Organic Cofactors for M0119

Type Identity Chain
Thiamine diphosphate TPP 2236 A Overview

Metal Cofactors for M0119

Type Het group Number Chain
iron SF4 2235 A Overview
iron SF4 2234 A Overview
iron SF4 2233 A Overview
magnesium MG 2238 A Overview

References

  1. E. Chabriere et al. (1999), Nat. Struct. Biol., 6, 182-190. Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate.
    Medline: 10048931
  2. E. Chabriere et al. (2001), Science, 294, 2559-2563. Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase.
    Medline: 11752578
  3. C. Cavazza et al. (2006), Structure, 14, 217-224. Flexibility of thiamine diphosphate revealed by kinetic crystallographic studies of the reaction of pyruvate-ferredoxin oxidoreductase with pyruvate.
    Medline: 16472741

Homologue information for M0119 (2c3m)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0274 pyruvate oxidase
1.2.3.3
1pow 3.40.50.970
0.6470.0871Compare
M0106 pyruvate dehydrogenase (acetyl-transferring)
1.2.4.1
1w85 3.40.50.970
3.40.50.920
0.76560.2034Compare
M0280 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)
1.2.4.4
1dtw 3.40.50.970
3.40.50.920
0.76560.1037Compare
M0219 transketolase
2.2.1.1
1trk 3.40.50.970
3.40.50.920
0.56370.0809Compare
M0289 acetolactate synthase
2.2.1.6
1n0h 3.40.50.970
0.85410.1285Compare
M0215 pyruvate decarboxylase
4.1.1.1
1pvd 3.40.50.970
0.58450.1619Compare
M0220 benzoylformate decarboxylase
4.1.1.7
1mcz 3.40.50.970
0.78570.1554Compare
M0221 benzoin aldolase
4.1.2.38
2ag0 3.40.50.970
0.77920.1457Compare

View a comparison of the other reactions in MACiE with the CATH domain 3.40.50.920

View a comparison of the other reactions in MACiE with the CATH domain 3.40.50.970


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

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catalytic activity (molecular function)
iron ion binding (molecular function)
transport (biological process)
metabolic process (biological process)
electron carrier activity (molecular function)
oxidoreductase activity (molecular function)
oxidoreductase activity, acting on the aldehyde or oxo group of donors (molecular function)
electron transport chain (biological process)
thiamine pyrophosphate binding (molecular function)
metal ion binding (molecular function)
iron-sulfur cluster binding (molecular function)
4 iron, 4 sulfur cluster binding (molecular function)
oxidation-reduction process (biological process)
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