spacer

Overview for MACiE Entry M0220

Version history

General Information

EC Number: 4.1.1.7 (A member of the Lyases, Carbon-carbon lyases, Carboxy-lyases)

Enzyme Name: benzoylformate decarboxylase

Biological Species: Pseudomonas putida (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • P20906 - Benzoylformate decarboxylase

Representative PDB Code: 1mcz - BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDACOMPLEXED WITH AN INHIBITOR, R-MANDELATE (Resolution = 2.80 Å).

Catalytic CATH Codes:

"Other" CATH Codes:

Display structure information

Overall Reaction:

Image of alpha-Oxo-benzeneacetic acid

right arrow

Image of Carbon dioxide

Image of Benzaldehyde

alpha-Oxo-benzeneacetic acid
C02137
CHEBI:18280
Carbon dioxide
C00011
CHEBI:16526
Benzaldehyde
C00261
CHEBI:17169

View similar reactions


Stepwise Description of the Reaction

Step 1Glu47B 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 attacks the carbonyl carbon of alpha-oxo-benzeneacetic acid in a nucleophilic addition. The formed oxyanion deprotonates His70B
Step 3Carbon dioxide eliminates from the covalently attached aromatic intermediate. Thiamine diphosphate acts as an electron sink.
Step 4Thiamine diphosphate initiates a double bond rearrangement, which results in the intermediate being protonated by His281A.
Step 5His70B deprotonates the hydroxide of the intermediate, which initiates an elimination which results in a reformation of the carbanionic activated cofactor and the benzaldehyde product.
Step 6The carbanion of the thiamine diphosphate cofactor deprotonates the adjacent amine, which initiates double bond rearrangement that results in the deprotonation of Glu47B. His281A deprotonates water.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Glu 47 B Side Chain
Glu 28 B Side Chain
His 70 B Side Chain
Ser 26 B Side Chain
Gly 401 A Main Chain Carbonyl
His 281 A Side Chain

Organic Cofactors for M0220

Type Identity Chain
Thiamine diphosphate TDP 533 A Overview

Metal Cofactors for M0220

Type Het group Number Chain
magnesium MG 529 A Overview

References

  1. E. S. Polovnikova et al. (2003), Biochemistry, 42, 1820-1830. Structural and kinetic analysis of catalysis by a thiamin diphosphate-dependent enzyme, benzoylformate decarboxylase.
    Medline: 12590569
  2. M. S. Hasson et al. (1998), Biochemistry, 37, 9918-9930. The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes.
    Medline: 9665697

Homologue information for M0220 (1mcz)

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
0.74610.1223Compare
M0106 pyruvate dehydrogenase (acetyl-transferring)
1.2.4.1
1w85 3.40.50.970
0.89470.4908Compare
M0280 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)
1.2.4.4
1dtw 3.40.50.970
0.89470.551Compare
M0119 pyruvate:ferredoxin oxidoreducatse
1.2.7.1
2c3m 3.40.50.970
0.78570.1554Compare
M0116 NAD(P)+ transhydrogenase (AB-specific)
1.6.1.2
1hzz 3.40.50.1220
0.30550Compare
M0219 transketolase
2.2.1.1
1trk 3.40.50.970
0.74830.6178Compare
M0289 acetolactate synthase
2.2.1.6
1n0h 3.40.50.970
3.40.50.1220
0.73910.1598Compare
M0240 histone/protein deacetylase
3.5.1.-
1szd 3.40.50.1220
0.46340.1170Compare
M0215 pyruvate decarboxylase
4.1.1.1
1pvd 3.40.50.970
3.40.50.1220
0.80280.7362Compare
M0221 benzoin aldolase
4.1.2.38
2ag0 3.40.50.970
0.97640.5260Compare

View a comparison of the other reactions in MACiE with the CATH domain 3.40.50.1220

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
Link to EzCatDB

GOA logo
magnesium ion binding (molecular function)
catalytic activity (molecular function)
transferase activity (molecular function)
lyase activity (molecular function)
carboxy-lyase activity (molecular function)
mandelate metabolic process (biological process)
aromatic compound catabolic process (biological process)
thiamine pyrophosphate binding (molecular function)
metal ion binding (molecular function)
benzoylformate decarboxylase activity (molecular function)
spacer
spacer