1bfd
From Proteopedia
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| - | [[Image:1bfd.gif|left|200px]] | + | [[Image:1bfd.gif|left|200px]] |
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| - | '''BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA''' | + | {{Structure |
| + | |PDB= 1bfd |SIZE=350|CAPTION= <scene name='initialview01'>1bfd</scene>, resolution 1.60Å | ||
| + | |SITE= <scene name='pdbsite=CA1:Divalent+Cation+Bound+To+Pyrophosphate+Of+Tpp+(Ca+529)'>CA1</scene>, <scene name='pdbsite=CA2:Ca+Ion+At+Crystal+Contact+(Ca+532)'>CA2</scene>, <scene name='pdbsite=MG1:Mg+Ion+On+Crystallographic+Two-Fold+At+Dimer+Interface+(+...'>MG1</scene> and <scene name='pdbsite=PP2:Polyproline+Type+II+Helix+From+ARG+334+Through+VAL+346'>PP2</scene> | ||
| + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=TPP:THIAMINE DIPHOSPHATE'>TPP</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Benzoylformate_decarboxylase Benzoylformate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.7 4.1.1.7] | ||
| + | |GENE= MDLC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida]) | ||
| + | }} | ||
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| + | '''BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA''' | ||
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==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1BFD is a [ | + | 1BFD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFD OCA]. |
==Reference== | ==Reference== | ||
| - | The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes., Hasson MS, Muscate A, McLeish MJ, Polovnikova LS, Gerlt JA, Kenyon GL, Petsko GA, Ringe D, Biochemistry. 1998 Jul 14;37(28):9918-30. PMID:[http:// | + | The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes., Hasson MS, Muscate A, McLeish MJ, Polovnikova LS, Gerlt JA, Kenyon GL, Petsko GA, Ringe D, Biochemistry. 1998 Jul 14;37(28):9918-30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9665697 9665697] |
[[Category: Benzoylformate decarboxylase]] | [[Category: Benzoylformate decarboxylase]] | ||
[[Category: Pseudomonas putida]] | [[Category: Pseudomonas putida]] | ||
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[[Category: thiamin diphosphate]] | [[Category: thiamin diphosphate]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:10:22 2008'' |
Revision as of 08:10, 20 March 2008
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| , resolution 1.60Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , and | ||||||
| Ligands: | , and | ||||||
| Gene: | MDLC (Pseudomonas putida) | ||||||
| Activity: | Benzoylformate decarboxylase, with EC number 4.1.1.7 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
Overview
The crystal structure of the thiamin diphosphate (ThDP)-dependent enzyme benzoylformate decarboxylase (BFD), the third enzyme in the mandelate pathway of Pseudomonas putida, has been solved by multiple isomorphous replacement at 1.6 A resolution and refined to an R-factor of 15.0% (free R = 18.6%). The structure of BFD has been compared to that of other ThDP-dependent enzymes, including pyruvate decarboxylase. The overall architecture of BFD resembles that of the other family members, and cofactor- and metal-binding residues are well conserved. Surprisingly, there is no conservation of active-site residues not directly bound to the cofactor. The position of functional groups in the active site may be conserved, however. Three classes of metal ions have been identified in the BFD crystal structure: Ca2+ bound to the cofactor in each subunit, Mg2+ on a 2-fold axis of the tetramer, and Ca2+ at a crystal contact. The structure includes a non-proline cis-peptide bond and an unusually long and regular polyproline type II helix that mediates the main contact between tetramers in the crystal. The high-quality electron-density map allowed the correction of errors totaling more than 10% of the amino acid sequence, which had been predicted from the reported sequence of the mdlC gene. Analysis of the BFD structure suggests that requirements for activation of the cofactor, the nature of the reaction intermediates, and architectural considerations relating to the protein fold have been dominant forces in the evolution of ThDP-dependent enzymes.
About this Structure
1BFD is a Single protein structure of sequence from Pseudomonas putida. Full crystallographic information is available from OCA.
Reference
The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes., Hasson MS, Muscate A, McLeish MJ, Polovnikova LS, Gerlt JA, Kenyon GL, Petsko GA, Ringe D, Biochemistry. 1998 Jul 14;37(28):9918-30. PMID:9665697
Page seeded by OCA on Thu Mar 20 10:10:22 2008
Categories: Benzoylformate decarboxylase | Pseudomonas putida | Single protein | Gerlt, J A. | Hasson, M S. | Kenyon, G L. | Mcleish, M J. | Muscate, A. | Petsko, G A. | Polovnikova, L S. | Ringe, D. | CA | MG | TPP | Carbon-carbon | Decarboxylase | Lyase | Mandelate catabolism | Thiamin diphosphate
