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1yno

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(New page: 200px<br /><applet load="1yno" size="450" color="white" frame="true" align="right" spinBox="true" caption="1yno, resolution 1.22&Aring;" /> '''High Resolution Stru...)
Current revision (06:59, 23 August 2023) (edit) (undo)
 
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[[Image:1yno.gif|left|200px]]<br /><applet load="1yno" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1yno, resolution 1.22&Aring;" />
 
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'''High Resolution Structure of Benzoylformate Decarboxylase from Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate'''<br />
 
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==Overview==
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==High Resolution Structure of Benzoylformate Decarboxylase from Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate==
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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.
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<StructureSection load='1yno' size='340' side='right'caption='[[1yno]], [[Resolution|resolution]] 1.22&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1yno]] 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=1YNO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YNO FirstGlance]. <br>
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1YNO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with MG, CA and TZD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YNO OCA].
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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]] 1.22&#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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TZD:2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TZD</scene></td></tr>
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==Reference==
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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=1yno FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yno OCA], [https://pdbe.org/1yno PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yno RCSB], [https://www.ebi.ac.uk/pdbsum/1yno PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yno ProSAT]</span></td></tr>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=9665697 9665697]
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</table>
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[[Category: Benzoylformate decarboxylase]]
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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/yn/1yno_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=1yno ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pseudomonas putida]]
[[Category: Pseudomonas putida]]
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[[Category: Single protein]]
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[[Category: Bera AK]]
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[[Category: Bera, A.K.]]
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[[Category: Hasson MS]]
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[[Category: Hasson, M.S.]]
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[[Category: CA]]
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[[Category: MG]]
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[[Category: TZD]]
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[[Category: carbon-carbon]]
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[[Category: decarboxylase]]
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[[Category: high resolution]]
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[[Category: lyase]]
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[[Category: mandelate catabolism]]
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[[Category: thiamine thiazolone diphosphate]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:56:09 2007''
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Current revision

High Resolution Structure of Benzoylformate Decarboxylase from Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate

PDB ID 1yno

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