EzCatDB: T00230
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DB codeT00230
RLCP classification5.105.3195000.7370 : Elimination
5.171.2330000.7370 : Elimination
CATH domainDomain 13.40.50.1220 : Rossmann foldCatalytic domain
Domain 23.40.50.970 : Rossmann foldCatalytic domain
Domain 33.40.50.970 : Rossmann fold
E.C.4.1.1.7
CSA1bfd
MACiEM0220

CATH domainRelated DB codes (homologues)
3.40.50.1220 : Rossmann foldM00162,M00161,T00237
3.40.50.970 : Rossmann foldT00210,T00237

Enzyme Name
UniProtKBKEGG

P20906
Protein nameBenzoylformate decarboxylasebenzoylformate decarboxylase
phenylglyoxylate decarboxylase
benzoylformate carboxy-lyase
SynonymsBFD
BFDC
EC 4.1.1.7
PfamPF02775 (TPP_enzyme_C)
PF00205 (TPP_enzyme_M)
PF02776 (TPP_enzyme_N)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00362Benzoate degradation via hydroxylation
MAP00622Toluene and xylene degradation

UniProtKB:Accession NumberP20906
Entry nameMDLC_PSEPU
ActivityBenzoylformate = benzaldehyde + CO(2).
SubunitHomotetramer.
Subcellular location
CofactorBinds 1 calcium ion per subunit.,Binds 1 thiamine pyrophosphate per subunit.,Binds 1 magnesium ion per dimer.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00068C00305C00076C02137C00261C00011
CompoundThiamine diphosphateMagnesiumCalciumBenzoylformateBenzaldehydeCO2
Typeamine group,aromatic ring (with nitrogen atoms),phosphate group/phosphate iondivalent metal (Ca2+, Mg2+)divalent metal (Ca2+, Mg2+)aromatic ring (only carbon atom),carbohydrate,carboxyl grouparomatic ring (only carbon atom),carbohydrateothers
ChEBI9532
18420
29108
18280
17169
16526
PubChem1132
888
271
11915
240
280
              
1bfdA01UnboundUnboundUnboundUnboundUnboundUnbound
1mczA01UnboundUnboundUnboundUnboundUnboundUnbound
1mczB01UnboundUnboundUnboundUnboundUnboundUnbound
1mczC01UnboundUnboundUnboundUnboundUnboundUnbound
1mczD01UnboundUnboundUnboundUnboundUnboundUnbound
1mczE01UnboundUnboundUnboundUnboundUnboundUnbound
1mczF01UnboundUnboundUnboundUnboundUnboundUnbound
1mczG01UnboundUnboundUnboundUnboundUnboundUnbound
1mczH01UnboundUnboundUnboundUnboundUnboundUnbound
1mczI01UnboundUnboundUnboundUnboundUnboundUnbound
1mczJ01UnboundUnboundUnboundUnboundUnboundUnbound
1mczK01UnboundUnboundUnboundUnboundUnboundUnbound
1mczL01UnboundUnboundUnboundUnboundUnboundUnbound
1mczM01UnboundUnboundUnboundUnboundUnboundUnbound
1mczN01UnboundUnboundUnboundUnboundUnboundUnbound
1mczO01UnboundUnboundUnboundUnboundUnboundUnbound
1mczP01UnboundUnboundUnboundUnboundUnboundUnbound
1bfdA02UnboundBound:_MGUnboundUnboundUnboundUnbound
1mczA02UnboundBound:_MGUnboundAnalogue:RMNUnboundUnbound
1mczB02UnboundUnboundUnboundAnalogue:RMNUnboundUnbound
1mczC02UnboundBound:_MGUnboundAnalogue:RMNUnboundUnbound
1mczD02UnboundUnboundUnboundAnalogue:RMNUnboundUnbound
1mczE02UnboundBound:_MGUnboundAnalogue:RMNUnboundUnbound
1mczF02UnboundUnboundUnboundAnalogue:RMNUnboundUnbound
1mczG02UnboundBound:_MGUnboundAnalogue:RMNUnboundUnbound
1mczH02UnboundUnboundUnboundAnalogue:RMNUnboundUnbound
1mczI02UnboundBound:_MGUnboundAnalogue:RMNUnboundUnbound
1mczJ02UnboundUnboundUnboundAnalogue:RMNUnboundUnbound
1mczK02UnboundBound:_MGUnboundAnalogue:RMNUnboundUnbound
1mczL02UnboundUnboundUnboundAnalogue:RMNUnboundUnbound
1mczM02UnboundBound:_MGUnboundAnalogue:RMNUnboundUnbound
1mczN02UnboundUnboundUnboundAnalogue:RMNUnboundUnbound
1mczO02UnboundBound:_MGUnboundAnalogue:RMNUnboundUnbound
1mczP02UnboundUnboundUnboundAnalogue:RMNUnboundUnbound
1bfdA03Bound:TPPUnboundBound:_CAUnboundUnboundUnbound
1mczA03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczB03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczC03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczD03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczE03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczF03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczG03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczH03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczI03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczJ03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczK03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczL03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczM03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczN03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczO03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound
1mczP03Bound:TDPUnboundAnalogue:_MGUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P20906 & literature [9]
pdbCatalytic residuesCofactor-binding residues
          
1bfdA01HIS 281
 
1mczA01HIS 281
 
1mczB01HIS 281
 
1mczC01HIS 281
 
1mczD01HIS 281
 
1mczE01HIS 281
 
1mczF01HIS 281
 
1mczG01HIS 281
 
1mczH01HIS 281
 
1mczI01HIS 281
 
1mczJ01HIS 281
 
1mczK01HIS 281
 
1mczL01HIS 281
 
1mczM01HIS 281
 
1mczN01HIS 281
 
1mczO01HIS 281
 
1mczP01HIS 281
 
1bfdA02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczA02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczB02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczC02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczD02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczE02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczF02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczG02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczH02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczI02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczJ02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczK02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczL02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczM02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczN02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczO02SER 26;GLU 47;HIS 70
ASN 117;LEU 118;ARG 120(magnesium binding)
1mczP02SER 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
ReferencesSectionsNo. of steps in catalysis
[3]

[5]Scheme 2, p.99194
[9]Fig.1, p.1827-18285

references
[1]
JournalChem Rev
Year1987
Volume87
Pages863-76
AuthorsKluger R
Title.
[2]
CommentsCHARACTERIZATION, AND CRYSTALLIZATION.
Medline ID95392398
PubMed ID7663351
JournalProtein Sci
Year1995
Volume4
Pages955-9
AuthorsHasson MS, Muscate A, Henehan GT, Guidinger PF, Petsko GA, Ringe D, Kenyon GL
TitlePurification and crystallization of benzoylformate decarboxylase.
Related UniProtKBP20906
[3]
JournalPure Appl Chem
Year1997
Volume69
Pages1957-67
AuthorsKluger R
TitleLessons from thiamin-watching
[4]
CommentsReview in a book; Academic Press Ltd., San Diego
JournalComprehensive Biological Catalysis (Editor: Sinnott M)
Year1998
Volume
Pages217-66
AuthorsSchowen RL
TitleThiamin-dependent Enzymes
[5]
CommentsX-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS), AND REVISIONS TO C-TERMINUS.
Medline ID98332515
PubMed ID9665697
JournalBiochemistry
Year1998
Volume37
Pages9918-30
AuthorsHasson MS, Muscate A, McLeish MJ, Polovnikova LS, Gerlt JA, Kenyon GL, Petsko GA, Ringe D
TitleThe crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes.
Related PDB1bfd
Related UniProtKBP20906
[6]
PubMed ID9655911
JournalBiochim Biophys Acta
Year1998
Volume1385
Pages229-43
AuthorsSchorken U, Sprenger GA
TitleThiamin-dependent enzymes as catalysts in chemoenzymatic syntheses.
[7]
PubMed ID12371834
JournalJ Am Chem Soc
Year2002
Volume124
Pages12084-5
AuthorsDunkelmann P, Kolter-Jung D, Nitsche A, Demir AS, Siegert P, Lingen B, Baumann M, Pohl M, Muller M
TitleDevelopment of a donor-acceptor concept for enzymatic cross-coupling reactions of aldehydes: the first asymmetric cross-benzoin condensation.
[8]
PubMed ID12432496
JournalChemistry
Year2002
Volume8
Pages5288-95
AuthorsPohl M, Lingen B, Muller M
TitleThiamin-diphosphate-dependent enzymes: new aspects of asymmetric C-C bond formation.
[9]
PubMed ID12590569
JournalBiochemistry
Year2003
Volume42
Pages1820-30
AuthorsPolovnikova ES, McLeish MJ, Sergienko EA, Burgner JT, Anderson NL, Bera AK, Jordan F, Kenyon GL, Hasson MS
TitleStructural and kinetic analysis of catalysis by a thiamin diphosphate-dependent enzyme, benzoylformate decarboxylase.
Related PDB1mcz

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.

createdupdated
2004-03-252009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
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