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| | ==Crystal structure of benzoylformate decarboxylase in complex with the inhibitor MBP== | | ==Crystal structure of benzoylformate decarboxylase in complex with the inhibitor MBP== |
| - | <StructureSection load='3fsj' size='340' side='right' caption='[[3fsj]], [[Resolution|resolution]] 1.37Å' scene=''> | + | <StructureSection load='3fsj' size='340' side='right'caption='[[3fsj]], [[Resolution|resolution]] 1.37Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3fsj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FSJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FSJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3fsj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FSJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FSJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=D7K:3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(S)-HYDROXY[(R)-HYDROXY(METHOXY)PHOSPHORYL]PHENYLMETHYL}-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM'>D7K</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.37Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3d7k|3d7k]], [[3f6b|3f6b]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=D7K:3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(S)-HYDROXY[(R)-HYDROXY(METHOXY)PHOSPHORYL]PHENYLMETHYL}-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM'>D7K</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mdlC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3fsj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fsj OCA], [https://pdbe.org/3fsj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fsj RCSB], [https://www.ebi.ac.uk/pdbsum/3fsj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fsj ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fsj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fsj OCA], [http://pdbe.org/3fsj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fsj RCSB], [http://www.ebi.ac.uk/pdbsum/3fsj PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/MDLC_PSEPU MDLC_PSEPU] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fs/3fsj_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fs/3fsj_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus fluorescens putidus flugge 1886]] | + | [[Category: Large Structures]] |
| - | [[Category: Benzoylformate decarboxylase]] | + | [[Category: Pseudomonas putida]] |
| - | [[Category: Brandt, G S]] | + | [[Category: Brandt GS]] |
| - | [[Category: Jordan, F]] | + | [[Category: Jordan F]] |
| - | [[Category: Kenyon, G L]] | + | [[Category: Kenyon GL]] |
| - | [[Category: McLeish, M J]] | + | [[Category: McLeish MJ]] |
| - | [[Category: Petsko, G A]] | + | [[Category: Petsko GA]] |
| - | [[Category: Ringe, D]] | + | [[Category: Ringe D]] |
| - | [[Category: Aromatic hydrocarbons catabolism]]
| + | |
| - | [[Category: Decarboxylase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Magnesium]]
| + | |
| - | [[Category: Mandelate pathway]]
| + | |
| - | [[Category: Metal binding]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Thiamin adduct]]
| + | |
| - | [[Category: Thiamine pyrophosphate]]
| + | |
| Structural highlights
Function
MDLC_PSEPU
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate- (ThDP-) dependent enzyme acting on aromatic substrates. In addition to its metabolic role in the mandelate pathway, BFDC shows broad substrate specificity coupled with tight stereo control in the carbon-carbon bond-forming reverse reaction, making it a useful biocatalyst for the production of chiral alpha-hydroxy ketones. The reaction of methyl benzoylphosphonate (MBP), an analogue of the natural substrate benzoylformate, with BFDC results in the formation of a stable analogue (C2alpha-phosphonomandelyl-ThDP) of the covalent ThDP-substrate adduct C2alpha-mandelyl-ThDP. Formation of the stable adduct is confirmed both by formation of a circular dichroism band characteristic of the 1',4'-iminopyrimidine tautomeric form of ThDP (commonly observed when ThDP forms tetrahedral complexes with its substrates) and by high-resolution mass spectrometry of the reaction mixture. In addition, the structure of BFDC with the MBP inhibitor was solved by X-ray crystallography to a spatial resolution of 1.37 A (PDB ID 3FSJ). The electron density clearly shows formation of a tetrahedral adduct between the C2 atom of ThDP and the carbonyl carbon atom of the MBP. This adduct resembles the intermediate from the penultimate step of the carboligation reaction between benzaldehyde and acetaldehyde. The combination of real-time kinetic information via stopped-flow circular dichroism with steady-state data from equilibrium circular dichroism measurements and X-ray crystallography reveals details of the first step of the reaction catalyzed by BFDC. The MBP-ThDP adduct on BFDC is compared to the recently solved structure of the same adduct on benzaldehyde lyase, another ThDP-dependent enzyme capable of catalyzing aldehyde condensation with high stereospecificity.
Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor.,Brandt GS, Kneen MM, Chakraborty S, Baykal AT, Nemeria N, Yep A, Ruby DI, Petsko GA, Kenyon GL, McLeish MJ, Jordan F, Ringe D Biochemistry. 2009 Apr 21;48(15):3247-57. PMID:19320438[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Brandt GS, Kneen MM, Chakraborty S, Baykal AT, Nemeria N, Yep A, Ruby DI, Petsko GA, Kenyon GL, McLeish MJ, Jordan F, Ringe D. Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor. Biochemistry. 2009 Apr 21;48(15):3247-57. PMID:19320438 doi:10.1021/bi801950k
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