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2v3w

From Proteopedia

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[[Image:2v3w.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of the benzoylformate decarboxylase variant L461A from Pseudomonas putida==
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|PDB= 2v3w |SIZE=350|CAPTION= <scene name='initialview01'>2v3w</scene>, resolution 2.20&Aring;
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<StructureSection load='2v3w' size='340' side='right'caption='[[2v3w]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Residue+A+1528'>AC1</scene>, <scene name='pdbsite=AC2:Mg+Binding+Site+For+Residue+A+1529'>AC2</scene>, <scene name='pdbsite=AC3:Mg+Binding+Site+For+Residue+B+1528'>AC3</scene>, <scene name='pdbsite=AC4:Mg+Binding+Site+For+Residue+B+1529'>AC4</scene>, <scene name='pdbsite=AC5:Mg+Binding+Site+For+Residue+C+1528'>AC5</scene>, <scene name='pdbsite=AC6:Mg+Binding+Site+For+Residue+D+1528'>AC6</scene>, <scene name='pdbsite=AC7:So4+Binding+Site+For+Residue+C+1529'>AC7</scene>, <scene name='pdbsite=AC8:So4+Binding+Site+For+Residue+D+1529'>AC8</scene>, <scene name='pdbsite=AC9:So4+Binding+Site+For+Residue+A+1530'>AC9</scene>, <scene name='pdbsite=BC1:So4+Binding+Site+For+Residue+B+1530'>BC1</scene>, <scene name='pdbsite=BC2:Tpp+Binding+Site+For+Residue+A+1531'>BC2</scene>, <scene name='pdbsite=BC3:Tpp+Binding+Site+For+Residue+B+1531'>BC3</scene>, <scene name='pdbsite=BC4:Tpp+Binding+Site+For+Residue+C+1530'>BC4</scene> and <scene name='pdbsite=BC5:Tpp+Binding+Site+For+Residue+D+1530'>BC5</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=TPP:THIAMINE DIPHOSPHATE'>TPP</scene>
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<table><tr><td colspan='2'>[[2v3w]] is a 4 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=2V3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V3W FirstGlance]. <br>
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|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]
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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]] 2.2&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
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}}
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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=2v3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v3w OCA], [https://pdbe.org/2v3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v3w RCSB], [https://www.ebi.ac.uk/pdbsum/2v3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v3w 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/v3/2v3w_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=2v3w 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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Benzoylformate decarboxylase (BFD) from Pseudomonas putida is an exceptional thiamin diphosphate-dependent enzyme, as it catalyzes the formation of (S)-2-hydroxy-1-phenylpropan-1-one from benzaldehyde and acetaldehyde. This is the only currently known S-selective reaction (92 % ee) catalyzed by this otherwise R-selective class of enzymes. Here we describe the molecular basis of the introduction of S selectivity into ThDP-dependent decarboxylases. By shaping the active site of BFD through the use of rational protein design, structural analysis, and molecular modeling, optimal steric stabilization of the acceptor aldehyde in a structural element called the S pocket was identified as the predominant interaction for adjusting stereoselectivity. Our studies revealed Leu461 as a hot spot for stereoselectivity in BFD. Exchange to alanine and glycine resulted in variants that catalyze the S-stereoselective addition of larger acceptor aldehydes, such as propanal with benzaldehyde and its derivatives-a reaction not catalyzed by the wild-type enzyme. Crystal structure analysis of the variant BFDL461A supports the modeling studies.
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'''CRYSTAL STRUCTURE OF THE BENZOYLFORMATE DECARBOXYLASE VARIANT L461A FROM PSEUDOMONAS PUTIDA'''
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Rational protein design of ThDP-dependent enzymes-engineering stereoselectivity.,Gocke D, Walter L, Gauchenova E, Kolter G, Knoll M, Berthold CL, Schneider G, Pleiss J, Muller M, Pohl M Chembiochem. 2008 Feb 15;9(3):406-12. PMID:18224647<ref>PMID:18224647</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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==About this Structure==
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</div>
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2V3W 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=2V3W OCA].
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<div class="pdbe-citations 2v3w" style="background-color:#fffaf0;"></div>
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[[Category: Benzoylformate decarboxylase]]
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== References ==
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<references/>
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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: Berthold CL]]
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[[Category: Berthold, C L.]]
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[[Category: Gauchenova K]]
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[[Category: Gauchenova, K.]]
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[[Category: Gocke D]]
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[[Category: Gocke, D.]]
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[[Category: Knoll M]]
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[[Category: Knoll, M.]]
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[[Category: Kolter G]]
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[[Category: Kolter, G.]]
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[[Category: Mueller M]]
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[[Category: Mueller, M.]]
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[[Category: Pleiss J]]
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[[Category: Pleiss, J.]]
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[[Category: Pohl M]]
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[[Category: Pohl, M.]]
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[[Category: Schneider G]]
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[[Category: Schneider, G.]]
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[[Category: Walter L]]
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[[Category: Walter, L.]]
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[[Category: MG]]
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[[Category: SO4]]
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[[Category: TPP]]
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[[Category: aromatic hydrocarbons catabolism]]
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[[Category: calcium]]
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[[Category: carboligation]]
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[[Category: decarboxylase]]
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[[Category: flavoprotein]]
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[[Category: lyase]]
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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: rational protein design]]
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[[Category: thdp-dependent]]
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[[Category: thiamine pyrophosphate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:43:00 2008''
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Current revision

Crystal structure of the benzoylformate decarboxylase variant L461A from Pseudomonas putida

PDB ID 2v3w

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