3f6e

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{{Seed}}
 
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[[Image:3f6e.png|left|200px]]
 
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==Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor 3-PKB==
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The line below this paragraph, containing "STRUCTURE_3f6e", creates the "Structure Box" on the page.
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<StructureSection load='3f6e' size='340' side='right'caption='[[3f6e]], [[Resolution|resolution]] 1.34&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3f6e]] 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=3F6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F6E FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.34&#8491;</td></tr>
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<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>
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{{STRUCTURE_3f6e| PDB=3f6e | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3f6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f6e OCA], [https://pdbe.org/3f6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f6e RCSB], [https://www.ebi.ac.uk/pdbsum/3f6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f6e ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/MDLC_PSEPU MDLC_PSEPU]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f6/3f6e_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3f6e ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor 3-PKB===
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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<ref>PMID:19140682</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_19140682}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3f6e" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19140682 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19140682}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3F6E 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=3F6E OCA].
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/19140682 19140682]
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[[Category: Benzoylformate decarboxylase]]
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[[Category: Pseudomonas putida]]
[[Category: Pseudomonas putida]]
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[[Category: Single protein]]
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[[Category: Brandt GS]]
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[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
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[[Category: Jordan F]]
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[[Category: Aromatic hydrocarbons catabolism]]
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[[Category: Kenyon GL]]
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[[Category: Calcium]]
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[[Category: McLeish MJ]]
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[[Category: Decarboxylase]]
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[[Category: Petsko GA]]
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[[Category: Lyase]]
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[[Category: Ringe D]]
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[[Category: Magnesium]]
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[[Category: Mandelate pathway]]
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[[Category: Metal-binding]]
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[[Category: Thiamin adduct]]
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[[Category: Thiamine pyrophosphate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 18 20:28:20 2009''
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Current revision

Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor 3-PKB

PDB ID 3f6e

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