2pzv

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(New page: 200px<br /><applet load="2pzv" size="450" color="white" frame="true" align="right" spinBox="true" caption="2pzv, resolution 1.250&Aring;" /> '''Crystal Structure o...)
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[[Image:2pzv.gif|left|200px]]<br /><applet load="2pzv" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2pzv, resolution 1.250&Aring;" />
 
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'''Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas Putida (pksi) with bound Phenol'''<br />
 
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==Overview==
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==Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas Putida (pksi) with bound Phenol==
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A longstanding proposal in enzymology is that enzymes are, electrostatically and geometrically complementary to the transition states, of the reactions they catalyze and that this complementarity contributes, to catalysis. Experimental evaluation of this contribution, however, has, been difficult. We have systematically dissected the potential, contribution to catalysis from electrostatic complementarity in, ketosteroid isomerase. Phenolates, analogs of the transition state and, reaction intermediate, bind and accept two hydrogen bonds in an active, site oxyanion hole. The binding of substituted phenolates of constant, molecular shape but increasing pK(a) models the charge accumulation in the, oxyanion hole during the enzymatic reaction. As charge localization, increases, the NMR chemical shifts of protons involved in oxyanion hole, hydrogen bonds increase by 0.50-0.76 ppm/pK(a) unit, suggesting a bond, shortening of 0.02 A/pK(a) unit. Nevertheless, there is little change in, binding affinity across a series of substituted phenolates (DeltaDeltaG =, -0.2 kcal/mol/pK(a) unit). The small effect of increased charge, localization on affinity occurs despite the shortening of the hydrogen, bonds and a large favorable change in binding enthalpy (DeltaDeltaH = -2.0, kcal/mol/pK(a) unit). This shallow dependence of binding affinity suggests, that electrostatic complementarity in the oxyanion hole makes at most a, modest contribution to catalysis of 300-fold. We propose that geometrical, complementarity between the oxyanion hole hydrogen-bond donors and the, transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess, through a combination of modest contributions from several mechanisms, rather than from a single dominant contribution.
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<StructureSection load='2pzv' size='340' side='right'caption='[[2pzv]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2pzv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2b32 2b32]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PZV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PZV FirstGlance]. <br>
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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]] 1.25&#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=IPH:PHENOL'>IPH</scene></td></tr>
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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=2pzv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pzv OCA], [https://pdbe.org/2pzv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pzv RCSB], [https://www.ebi.ac.uk/pdbsum/2pzv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pzv ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SDIS_PSEPU SDIS_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/pz/2pzv_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=2pzv ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2PZV 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 IPH as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 2B32. Active as [http://en.wikipedia.org/wiki/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2PZV OCA].
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*[[Ketosteroid Isomerase|Ketosteroid Isomerase]]
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__TOC__
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==Reference==
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</StructureSection>
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Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole., Kraut DA, Sigala PA, Pybus B, Liu CW, Ringe D, Petsko GA, Herschlag D, PLoS Biol. 2006 Apr;4(4):e99. Epub 2006 Mar 28. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16602823 16602823]
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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: Caaveiro JMM]]
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[[Category: Steroid Delta-isomerase]]
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[[Category: Petsko GA]]
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[[Category: Caaveiro, J.M.M.]]
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[[Category: Pybus B]]
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[[Category: Petsko, G.A.]]
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[[Category: Ringe D]]
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[[Category: Pybus, B.]]
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[[Category: Ringe, D.]]
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[[Category: IPH]]
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[[Category: transition state analog bound]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:44:36 2007''
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Current revision

Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas Putida (pksi) with bound Phenol

PDB ID 2pzv

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