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Enzyme Name | UniProtKB | KEGG |
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| P20906 |
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Protein name | Benzoylformate decarboxylase | benzoylformate decarboxylasephenylglyoxylate decarboxylasebenzoylformate carboxy-lyase |
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Synonyms | BFDBFDCEC 4.1.1.7 |
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Pfam | PF02775 (TPP_enzyme_C) PF00205 (TPP_enzyme_M) PF02776 (TPP_enzyme_N) [Graphical view]
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KEGG pathways | MAP code | Pathways |
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MAP00362 | Benzoate degradation via hydroxylation | MAP00622 | Toluene and xylene degradation |
UniProtKB:Accession Number | P20906 |
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Entry name | MDLC_PSEPU |
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Activity | Benzoylformate = benzaldehyde + CO(2). |
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Subunit | Homotetramer. |
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Subcellular location |
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Cofactor | Binds 1 calcium ion per subunit.,Binds 1 thiamine pyrophosphate per subunit.,Binds 1 magnesium ion per dimer. |
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Compound table: links to PDB-related databases & PoSSuM |
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| Cofactors | Substrates | Products |
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KEGG-id | C00068 | C00305 | C00076 | C02137 | C00261 | C00011 |
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Compound | Thiamine diphosphate | Magnesium | Calcium | Benzoylformate | Benzaldehyde | CO2 |
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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 |
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ChEBI | 9532
| 18420
| 29108
| 18280
| 17169
| 16526
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PubChem | 1132
| 888
| 271
| 11915
| 240
| 280
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| | | | | | | | | | | | | |
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1bfdA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczB01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczC01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczD01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczE01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczF01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczG01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczH01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczI01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczJ01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczK01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczL01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczM01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczN01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczO01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1mczP01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1bfdA02 |  |  |  |  |  |  |  | Unbound | Bound:_MG | Unbound | Unbound | Unbound | Unbound |
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1mczA02 |  |  |  |  |  |  |  | Unbound | Bound:_MG | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczC02 |  |  |  |  |  |  |  | Unbound | Bound:_MG | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczD02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczE02 |  |  |  |  |  |  |  | Unbound | Bound:_MG | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczF02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczG02 |  |  |  |  |  |  |  | Unbound | Bound:_MG | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczH02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczI02 |  |  |  |  |  |  |  | Unbound | Bound:_MG | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczJ02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczK02 |  |  |  |  |  |  |  | Unbound | Bound:_MG | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczL02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczM02 |  |  |  |  |  |  |  | Unbound | Bound:_MG | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczN02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczO02 |  |  |  |  |  |  |  | Unbound | Bound:_MG | Unbound | Analogue:RMN | Unbound | Unbound |
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1mczP02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Analogue:RMN | Unbound | Unbound |
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1bfdA03 |  |  |  |  |  |  |  | Bound:TPP | Unbound | Bound:_CA | Unbound | Unbound | Unbound |
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1mczA03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczB03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczC03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczD03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczE03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczF03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczG03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczH03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczI03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczJ03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczK03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczL03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczM03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczN03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczO03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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1mczP03 |  |  |  |  |  |  |  | Bound:TDP | Unbound | Analogue:_MG | Unbound | Unbound | Unbound |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[3] |
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| [5] | Scheme 2, p.9919 | 4 | [9] | Fig.1, p.1827-1828 | 5 |
references | [1] |
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Journal | Chem Rev |
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Year | 1987 |
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Volume | 87 |
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Pages | 863-76 |
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Authors | Kluger R |
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Title | . |
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[2] |
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Comments | CHARACTERIZATION, AND CRYSTALLIZATION. |
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Medline ID | 95392398 |
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PubMed ID | 7663351 |
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Journal | Protein Sci |
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Year | 1995 |
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Volume | 4 |
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Pages | 955-9 |
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Authors | Hasson MS, Muscate A, Henehan GT, Guidinger PF, Petsko GA, Ringe D, Kenyon GL |
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Title | Purification and crystallization of benzoylformate decarboxylase. |
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Related UniProtKB | P20906 |
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[3] |
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Journal | Pure Appl Chem |
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Year | 1997 |
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Volume | 69 |
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Pages | 1957-67 |
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Authors | Kluger R |
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Title | Lessons from thiamin-watching |
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[4] |
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Comments | Review in a book; Academic Press Ltd., San Diego |
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Journal | Comprehensive Biological Catalysis (Editor: Sinnott M) |
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Year | 1998 |
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Volume |
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Pages | 217-66 |
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Authors | Schowen RL |
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Title | Thiamin-dependent Enzymes |
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[5] |
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Comments | X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS), AND REVISIONS TO C-TERMINUS. |
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Medline ID | 98332515 |
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PubMed ID | 9665697 |
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Journal | Biochemistry |
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Year | 1998 |
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Volume | 37 |
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Pages | 9918-30 |
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Authors | Hasson MS, Muscate A, McLeish MJ, Polovnikova LS, Gerlt JA, Kenyon GL, Petsko GA, Ringe D |
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Title | The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes. |
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Related PDB | 1bfd |
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Related UniProtKB | P20906 |
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[6] |
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PubMed ID | 9655911 |
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Journal | Biochim Biophys Acta |
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Year | 1998 |
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Volume | 1385 |
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Pages | 229-43 |
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Authors | Schorken U, Sprenger GA |
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Title | Thiamin-dependent enzymes as catalysts in chemoenzymatic syntheses. |
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[7] |
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PubMed ID | 12371834 |
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Journal | J Am Chem Soc |
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Year | 2002 |
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Volume | 124 |
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Pages | 12084-5 |
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Authors | Dunkelmann P, Kolter-Jung D, Nitsche A, Demir AS, Siegert P, Lingen B, Baumann M, Pohl M, Muller M |
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Title | Development of a donor-acceptor concept for enzymatic cross-coupling reactions of aldehydes: the first asymmetric cross-benzoin condensation. |
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[8] |
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PubMed ID | 12432496 |
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Journal | Chemistry |
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Year | 2002 |
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Volume | 8 |
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Pages | 5288-95 |
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Authors | Pohl M, Lingen B, Muller M |
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Title | Thiamin-diphosphate-dependent enzymes: new aspects of asymmetric C-C bond formation. |
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[9] |
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PubMed ID | 12590569 |
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Journal | Biochemistry |
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Year | 2003 |
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Volume | 42 |
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Pages | 1820-30 |
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Authors | Polovnikova ES, McLeish MJ, Sergienko EA, Burgner JT, Anderson NL, Bera AK, Jordan F, Kenyon GL, Hasson MS |
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Title | Structural and kinetic analysis of catalysis by a thiamin diphosphate-dependent enzyme, benzoylformate decarboxylase. |
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Related PDB | 1mcz |
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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.
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created | updated |
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2004-03-25 | 2009-02-26 |
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