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| | ==Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor PAA== | | ==Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor PAA== |
| - | <StructureSection load='3f6b' size='340' side='right' caption='[[3f6b]], [[Resolution|resolution]] 1.34Å' scene=''> | + | <StructureSection load='3f6b' size='340' side='right'caption='[[3f6b]], [[Resolution|resolution]] 1.34Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3f6b]] 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=3F6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F6B FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3f6b]] 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=3F6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F6B FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8PA:3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-[(1S,2E)-1-HYDROXY-3-PYRIDIN-3-YLPROP-2-EN-1-YL]-4-METHYL-1,3-THIAZOL-3-IUM'>8PA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.34Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3f6e|3f6e]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8PA:3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-[(1S,2E)-1-HYDROXY-3-PYRIDIN-3-YLPROP-2-EN-1-YL]-4-METHYL-1,3-THIAZOL-3-IUM'>8PA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3f6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f6b OCA], [https://pdbe.org/3f6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f6b RCSB], [https://www.ebi.ac.uk/pdbsum/3f6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f6b 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=3f6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f6b OCA], [http://pdbe.org/3f6b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3f6b RCSB], [http://www.ebi.ac.uk/pdbsum/3f6b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3f6b ProSAT]</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/f6/3f6b_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f6/3f6b_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: Calcium]]
| + | |
| - | [[Category: Decarboxylase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Magnesium]]
| + | |
| - | [[Category: Mandelate pathway]]
| + | |
| - | [[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
The mechanism of the enzyme benzoylformate decarboxylase (BFDC), which carries out a typical thiamin diphosphate (ThDP)-dependent nonoxidative decarboxylation reaction, was studied with the chromophoric alternate substrate (E)-2-oxo-4(pyridin-3-yl)-3-butenoic acid (3-PKB). Addition of 3-PKB resulted in the appearance of two transient intermediates formed consecutively, the first one to be formed a predecarboxylation ThDP-bound intermediate with lambda(max) at 477 nm, and the second one corresponding to the first postdecarboxylation intermediate the enamine with lambda(max) at 437 nm. The time course of formation/depletion of the PKB-ThDP covalent complex and of the enamine showed that decarboxylation was slower than formation of the PKB-ThDP covalent adduct. When the product of decarboxylation 3-(pyridin-3-yl)acrylaldehyde (PAA) was added to BFDC, again an absorbance with lambda(max) at 473 nm was formed, corresponding to the tetrahedral adduct of PAA with ThDP. Addition of well-formed crystals of BFDC to a solution of PAA resulted in a high resolution (1.34 A) structure of the BFDC-bound adduct of ThDP with PAA confirming the tetrahedral nature at the C2alpha atom, rather than of the enamine, and supporting the assignment of the lambda(max) at 473 nm to the PAA-ThDP adduct. The structure of the PAA-ThDP covalent complex is the first example of a product-ThDP adduct on BFDC. Similar studies with 3-PKB indicated that decarboxylation had taken place. Evidence was also obtained for the slow formation of the enamine intermediate when BFDC was incubated with benzaldehyde, the product of the decarboxylation reaction thus confirming its presence on the reaction pathway.
Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase.,Chakraborty S, Nemeria NS, Balakrishnan A, Brandt GS, Kneen MM, Yep A, McLeish MJ, Kenyon GL, Petsko GA, Ringe D, Jordan F Biochemistry. 2009 Feb 10;48(5):981-94. PMID:19140682[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Chakraborty S, Nemeria NS, Balakrishnan A, Brandt GS, Kneen MM, Yep A, McLeish MJ, Kenyon GL, Petsko GA, Ringe D, Jordan F. Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase. Biochemistry. 2009 Feb 10;48(5):981-94. PMID:19140682 doi:10.1021/bi801810h
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