2pzv: Difference between revisions

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<StructureSection load='2pzv' size='340' side='right'caption='[[2pzv]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
<StructureSection load='2pzv' size='340' side='right'caption='[[2pzv]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2pzv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. 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>
<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>
</td></tr><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>
</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>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ksi ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
<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>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1] </span></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=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>
<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>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SDIS_PSEPU SDIS_PSEPU]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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].
</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="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:16602823<ref>PMID:16602823</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2pzv" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ketosteroid Isomerase|Ketosteroid Isomerase]]
*[[Ketosteroid Isomerase|Ketosteroid Isomerase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus fluorescens putidus flugge 1886]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Steroid Delta-isomerase]]
[[Category: Pseudomonas putida]]
[[Category: Caaveiro, J M.M]]
[[Category: Caaveiro JMM]]
[[Category: Petsko, G A]]
[[Category: Petsko GA]]
[[Category: Pybus, B]]
[[Category: Pybus B]]
[[Category: Ringe, D]]
[[Category: Ringe D]]
[[Category: Isomerase]]
[[Category: Transition state analog bound]]
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