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| - | [[Image:2pzv.gif|left|200px]] | |
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| - | {{Structure
| + | ==Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas Putida (pksi) with bound Phenol== |
| - | |PDB= 2pzv |SIZE=350|CAPTION= <scene name='initialview01'>2pzv</scene>, resolution 1.250Å
| + | <StructureSection load='2pzv' size='340' side='right'caption='[[2pzv]], [[Resolution|resolution]] 1.25Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=IPH:PHENOL'>IPH</scene>
| + | <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> |
| - | |ACTIVITY= <span class='plainlinks'>[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] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.25Å</td></tr> |
| - | |GENE= ksi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida])
| + | <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> |
| - | |DOMAIN=
| + | <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> |
| - | |RELATEDENTRY= | + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pzv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pzv OCA], [http://www.ebi.ac.uk/pdbsum/2pzv PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pzv RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/SDIS_PSEPU SDIS_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/pz/2pzv_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=2pzv ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | '''Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas Putida (pksi) with bound Phenol'''
| + | ==See Also== |
| - | | + | *[[Ketosteroid Isomerase|Ketosteroid Isomerase]] |
| - | | + | __TOC__ |
| - | ==Overview== | + | </StructureSection> |
| - | 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.
| + | [[Category: Large Structures]] |
| - | | + | |
| - | ==About this Structure==
| + | |
| - | 2PZV is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. This structure supersedes the now removed PDB entry 2B32. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PZV OCA].
| + | |
| - | | + | |
| - | ==Reference==
| + | |
| - | 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://www.ncbi.nlm.nih.gov/pubmed/16602823 16602823]
| + | |
| | [[Category: Pseudomonas putida]] | | [[Category: Pseudomonas putida]] |
| - | [[Category: Single protein]]
| + | [[Category: Caaveiro JMM]] |
| - | [[Category: Steroid Delta-isomerase]]
| + | [[Category: Petsko GA]] |
| - | [[Category: Caaveiro, J M.M.]] | + | [[Category: Pybus B]] |
| - | [[Category: Petsko, G A.]] | + | [[Category: Ringe D]] |
| - | [[Category: Pybus, B.]] | + | |
| - | [[Category: Ringe, D.]] | + | |
| - | [[Category: transition state analog bound]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:42:49 2008''
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