DB code: T00230

RLCP classification 5.105.3195000.7370 : Elimination
5.171.2330000.7370 : Elimination
CATH domain 3.40.50.1220 : Rossmann fold Catalytic domain
3.40.50.970 : Rossmann fold Catalytic domain
3.40.50.970 : Rossmann fold
E.C. 4.1.1.7
CSA 1bfd
M-CSA 1bfd
MACiE M0220

CATH domain Related DB codes (homologues)
3.40.50.1220 : Rossmann fold M00162 M00161 T00237
3.40.50.970 : Rossmann fold T00210 T00237

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P20906 Benzoylformate decarboxylase
BFD
BFDC
EC 4.1.1.7
PF02775 (TPP_enzyme_C)
PF00205 (TPP_enzyme_M)
PF02776 (TPP_enzyme_N)
[Graphical View]

KEGG enzyme name
benzoylformate decarboxylase
phenylglyoxylate decarboxylase
benzoylformate carboxy-lyase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P20906 MDLC_PSEPU Benzoylformate = benzaldehyde + CO(2). Homotetramer. Binds 1 calcium ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Binds 1 magnesium ion per dimer.

KEGG Pathways
Map code Pathways E.C.
MAP00362 Benzoate degradation via hydroxylation
MAP00622 Toluene and xylene degradation

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00068 C00305 C00076 C02137 C00261 C00011
E.C.
Compound Thiamine diphosphate Magnesium Calcium Benzoylformate Benzaldehyde CO2
Type amine group,aromatic ring (with nitrogen atoms),phosphate group/phosphate ion divalent metal (Ca2+, Mg2+) divalent metal (Ca2+, Mg2+) aromatic ring (only carbon atom),carbohydrate,carboxyl group aromatic ring (only carbon atom),carbohydrate others
ChEBI 9532
 9532
 		18420
 18420
 		29108
 29108
 		18280
 18280
 		17169
 17169
 		16526
 16526
PubChem 1132
 1132
 		888
 888
 		271
 271
 		11915
 11915
 		240
 240
 		280
 280
1bfdA01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczA01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczB01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczC01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczD01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczE01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczF01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczG01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczH01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczI01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczJ01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczK01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczL01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczM01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczN01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczO01 Unbound Unbound Unbound Unbound Unbound Unbound
1mczP01 Unbound Unbound Unbound Unbound Unbound Unbound
1bfdA02 Unbound Bound:_MG Unbound Unbound Unbound Unbound
1mczA02 Unbound Bound:_MG Unbound Analogue:RMN Unbound Unbound
1mczB02 Unbound Unbound Unbound Analogue:RMN Unbound Unbound
1mczC02 Unbound Bound:_MG Unbound Analogue:RMN Unbound Unbound
1mczD02 Unbound Unbound Unbound Analogue:RMN Unbound Unbound
1mczE02 Unbound Bound:_MG Unbound Analogue:RMN Unbound Unbound
1mczF02 Unbound Unbound Unbound Analogue:RMN Unbound Unbound
1mczG02 Unbound Bound:_MG Unbound Analogue:RMN Unbound Unbound
1mczH02 Unbound Unbound Unbound Analogue:RMN Unbound Unbound
1mczI02 Unbound Bound:_MG Unbound Analogue:RMN Unbound Unbound
1mczJ02 Unbound Unbound Unbound Analogue:RMN Unbound Unbound
1mczK02 Unbound Bound:_MG Unbound Analogue:RMN Unbound Unbound
1mczL02 Unbound Unbound Unbound Analogue:RMN Unbound Unbound
1mczM02 Unbound Bound:_MG Unbound Analogue:RMN Unbound Unbound
1mczN02 Unbound Unbound Unbound Analogue:RMN Unbound Unbound
1mczO02 Unbound Bound:_MG Unbound Analogue:RMN Unbound Unbound
1mczP02 Unbound Unbound Unbound Analogue:RMN Unbound Unbound
1bfdA03 Bound:TPP Unbound Bound:_CA Unbound Unbound Unbound
1mczA03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczB03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczC03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczD03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczE03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczF03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczG03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczH03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczI03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczJ03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczK03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczL03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczM03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczN03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczO03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound
1mczP03 Bound:TDP Unbound Analogue:_MG Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P20906 & literature [9]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bfdA01 HIS 281
1mczA01 HIS 281
1mczB01 HIS 281
1mczC01 HIS 281
1mczD01 HIS 281
1mczE01 HIS 281
1mczF01 HIS 281
1mczG01 HIS 281
1mczH01 HIS 281
1mczI01 HIS 281
1mczJ01 HIS 281
1mczK01 HIS 281
1mczL01 HIS 281
1mczM01 HIS 281
1mczN01 HIS 281
1mczO01 HIS 281
1mczP01 HIS 281
1bfdA02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczA02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczB02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczC02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczD02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczE02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczF02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczG02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczH02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczI02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczJ02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczK02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczL02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczM02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczN02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczO02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1mczP02 SER 26;GLU 47;HIS 70 ASN 117;LEU 118;ARG 120(magnesium binding)
1bfdA03 ASP 428;ASN 455;THR 457(calcium binding)
1mczA03 ASP 428;ASN 455;THR 457(calcium binding)
1mczB03 ASP 428;ASN 455;THR 457(calcium binding)
1mczC03 ASP 428;ASN 455;THR 457(calcium binding)
1mczD03 ASP 428;ASN 455;THR 457(calcium binding)
1mczE03 ASP 428;ASN 455;THR 457(calcium binding)
1mczF03 ASP 428;ASN 455;THR 457(calcium binding)
1mczG03 ASP 428;ASN 455;THR 457(calcium binding)
1mczH03 ASP 428;ASN 455;THR 457(calcium binding)
1mczI03 ASP 428;ASN 455;THR 457(calcium binding)
1mczJ03 ASP 428;ASN 455;THR 457(calcium binding)
1mczK03 ASP 428;ASN 455;THR 457(calcium binding)
1mczL03 ASP 428;ASN 455;THR 457(calcium binding)
1mczM03 ASP 428;ASN 455;THR 457(calcium binding)
1mczN03 ASP 428;ASN 455;THR 457(calcium binding)
1mczO03 ASP 428;ASN 455;THR 457(calcium binding)
1mczP03 ASP 428;ASN 455;THR 457(calcium binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
[5]
Scheme 2, p.9919 4
[9]
Fig.1, p.1827-1828 5

References
[1]
Resource
Comments
Medline ID
PubMed ID
Journal Chem Rev
Year 1987
Volume 87
Pages 863-76
Authors Kluger R
Title .
Related PDB
Related UniProtKB
[2]
Resource
Comments CHARACTERIZATION, AND CRYSTALLIZATION.
Medline ID 95392398
PubMed ID 7663351
Journal Protein Sci
Year 1995
Volume 4
Pages 955-9
Authors Hasson MS, Muscate A, Henehan GT, Guidinger PF, Petsko GA, Ringe D, Kenyon GL
Title Purification and crystallization of benzoylformate decarboxylase.
Related PDB
Related UniProtKB P20906
[3]
Resource
Comments
Medline ID
PubMed ID
Journal Pure Appl Chem
Year 1997
Volume 69
Pages 1957-67
Authors Kluger R
Title Lessons from thiamin-watching
Related PDB
Related UniProtKB
[4]
Resource
Comments Review in a book; Academic Press Ltd., San Diego
Medline ID
PubMed ID
Journal Comprehensive Biological Catalysis (Editor: Sinnott M)
Year 1998
Volume
Pages 217-66
Authors Schowen RL
Title Thiamin-dependent Enzymes
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS), AND REVISIONS TO C-TERMINUS.
Medline ID 98332515
PubMed ID 9665697
Journal Biochemistry
Year 1998
Volume 37
Pages 9918-30
Authors Hasson MS, Muscate A, McLeish MJ, Polovnikova LS, Gerlt JA, Kenyon GL, Petsko GA, Ringe D
Title The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes.
Related PDB 1bfd
Related UniProtKB P20906
[6]
Resource
Comments
Medline ID
PubMed ID 9655911
Journal Biochim Biophys Acta
Year 1998
Volume 1385
Pages 229-43
Authors Schorken U, Sprenger GA
Title Thiamin-dependent enzymes as catalysts in chemoenzymatic syntheses.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 12371834
Journal J Am Chem Soc
Year 2002
Volume 124
Pages 12084-5
Authors Dunkelmann P, Kolter-Jung D, Nitsche A, Demir AS, Siegert P, Lingen B, Baumann M, Pohl M, Muller M
Title Development of a donor-acceptor concept for enzymatic cross-coupling reactions of aldehydes: the first asymmetric cross-benzoin condensation.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 12432496
Journal Chemistry
Year 2002
Volume 8
Pages 5288-95
Authors Pohl M, Lingen B, Muller M
Title Thiamin-diphosphate-dependent enzymes: new aspects of asymmetric C-C bond formation.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 12590569
Journal Biochemistry
Year 2003
Volume 42
Pages 1820-30
Authors Polovnikova ES, McLeish MJ, Sergienko EA, Burgner JT, Anderson NL, Bera AK, Jordan F, Kenyon GL, Hasson MS
Title Structural and kinetic analysis of catalysis by a thiamin diphosphate-dependent enzyme, benzoylformate decarboxylase.
Related PDB 1mcz
Related UniProtKB

Comments
Although calcium ion and magnesium ion have been annotated as cofactors, they are not directly involved in catalysis. The calcium ion, which is bound per subunit, is bound to the diphosphate group of the organic cofactor, thiamin diphosphate. The magnesium ion, which is bound per dimer, is bound to the interface of two adjacent chains, away from the active site. Thus, thiamin diphosphate (ThDP) is only involved in the catalytic reaction.
According to the literature [5] & [9], the catalytic reaction proceeds, as follows;
(A) Addition of ThDP to carbonyl carbon of substrate:
(A1) The C4' imino group of the organic cofactor, ThDP, activates the C2 atom of ThDP by abstracting a proton from the C2 atom, forming an ylide group.
(A2) The ylide group makes a nucleophilic attack on the carbonyl carbon of the substrate to form a covalent bond between the cofactor, ThDP, and the substrate, reulting in the formation of the 1st tetrahedral intermediate, 2-alpha-mandelyl-ThDP. At this step, His70 seems to act as a general acid to protonate the carbonyl oxygen, to form a hydroxyl group.
(B) Elimination of carbon dioxide from the intermediate:
(B1) Decarboxylation from the intermediate results in the 2nd intermediate, a carbanion intermediate, stabilized by the resonance form, an enamine intermediate. (The enamine intermediate has a double-bond between the cofactor and substrate, whilst the carbanion intermediate has a single-bond between them.)
(B2) His281 seems to act as another general acid, to protonate the 2-alpha-carbanion, providing the 3rd tetrahedral intermediate, 2-alpha-hydroxybenzyl-ThDP.
(C) Elimination of ThDP from the 3rd intermediate:
(C1) His70 seems to act as a general base, which abstracts a proton from the hydroxyl group of the tetrahedral intermediate, facilitating the elimination of the benzaldehyde from ThDP.
Thus, the catalytic reaction proceeds through three intermediates. During catalysis, Ser26 assists the reactions, such as nucleophilic attack by the ylide, decarboxylation and elimination of ThDP.

Created Updated
2004-03-25 2009-02-26