2v3w: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2v3w.jpg|left|200px]]<br /><applet load="2v3w" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2v3w, resolution 2.20&Aring;" />
'''CRYSTAL STRUCTURE OF THE BENZOYLFORMATE DECARBOXYLASE VARIANT L461A FROM PSEUDOMONAS PUTIDA'''<br />


==About this Structure==
==Crystal structure of the benzoylformate decarboxylase variant L461A from Pseudomonas putida==
2V3W 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 <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=TPP:'>TPP</scene> 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] Known structural/functional Sites: <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>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V3W OCA].  
<StructureSection load='2v3w' size='340' side='right'caption='[[2v3w]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
[[Category: Benzoylformate decarboxylase]]
== Structural highlights ==
<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>
</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>
<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>
<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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MDLC_PSEPU MDLC_PSEPU]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v3/2v3w_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2v3w" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pseudomonas putida]]
[[Category: Pseudomonas putida]]
[[Category: Single protein]]
[[Category: Berthold CL]]
[[Category: Berthold, C L.]]
[[Category: Gauchenova K]]
[[Category: Gauchenova, K.]]
[[Category: Gocke D]]
[[Category: Gocke, D.]]
[[Category: Knoll M]]
[[Category: Knoll, M.]]
[[Category: Kolter G]]
[[Category: Kolter, G.]]
[[Category: Mueller M]]
[[Category: Mueller, M.]]
[[Category: Pleiss J]]
[[Category: Pleiss, J.]]
[[Category: Pohl M]]
[[Category: Pohl, M.]]
[[Category: Schneider G]]
[[Category: Schneider, G.]]
[[Category: Walter L]]
[[Category: Walter, L.]]
[[Category: MG]]
[[Category: SO4]]
[[Category: TPP]]
[[Category: aromatic hydrocarbons catabolism]]
[[Category: calcium]]
[[Category: carboligation]]
[[Category: decarboxylase]]
[[Category: flavoprotein]]
[[Category: lyase]]
[[Category: magnesium]]
[[Category: mandelate pathway]]
[[Category: metal-binding]]
[[Category: rational protein design]]
[[Category: thdp-dependent]]
[[Category: thiamine pyrophosphate]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:53:02 2008''
Retrieved from "https://proteopedia.org/2v3w"