1ogx: Difference between revisions

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-{{Seed}}
-[[Image:1ogx.png|left|200px]]
-<!--
+==High Resolution Crystal Structure Of Ketosteroid Isomerase Mutant D40N(D38N, Ti Numbering) from Pseudomonas putida Complexed With Equilenin At 2.0 A Resolution.==
-The line below this paragraph, containing "STRUCTURE_1ogx", creates the "Structure Box" on the page.
+<StructureSection load='1ogx' size='340' side='right'caption='[[1ogx]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1ogx]] is a 2 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=1e3n 1e3n]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OGX FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EQU:EQUILENIN'>EQU</scene></td></tr>
-{{STRUCTURE_1ogx|  PDB=1ogx  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ogx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogx OCA], [https://pdbe.org/1ogx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ogx RCSB], [https://www.ebi.ac.uk/pdbsum/1ogx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ogx ProSAT]</span></td></tr>
+</table>
+== 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/og/1ogx_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=1ogx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Delta(5)-3-Ketosteroid isomerase catalyzes cleavage and formation of a C-H bond at a diffusion-controlled limit. By determining the crystal structures of the enzyme in complex with each of three different inhibitors and by nuclear magnetic resonance (NMR) spectroscopic investigation, we evidenced the ionization of a hydroxyl group (pK(a) approximately 16.5) of an inhibitor, which forms a low barrier hydrogen bond (LBHB) with a catalytic residue Tyr(14) (pK(a) approximately 11.5), and the protonation of the catalytic residue Asp(38) with pK(a) of approximately 4.5 at pH 6.7 in the interaction with a carboxylate group of an inhibitor. The perturbation of the pK(a) values in both cases arises from the formation of favorable interactions between inhibitors and catalytic residues. The results indicate that the pK(a) difference between catalytic residue and substrate can be significantly reduced in the active site environment as a result of the formation of energetically favorable interactions during the course of enzyme reactions. The reduction in the pK(a) difference should facilitate the abstraction of a proton and thereby eliminate a large fraction of activation energy in general acid/base enzyme reactions. The pK(a) perturbation provides a mechanistic ground for the fast reactivity of many enzymes and for the understanding of how some enzymes are able to extract a proton from a C-H group with a pK(a) value as high as approximately 30.
-===HIGH RESOLUTION CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE MUTANT D40N(D38N, TI NUMBERING) FROM PSEUDOMONAS PUTIDA COMPLEXED WITH EQUILENIN AT 2.0 A RESOLUTION.===
+Detection of large pKa perturbations of an inhibitor and a catalytic group at an enzyme active site, a mechanistic basis for catalytic power of many enzymes.,Ha NC, Kim MS, Lee W, Choi KY, Oh BH J Biol Chem. 2000 Dec 29;275(52):41100-6. PMID:11007792<ref>PMID:11007792</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ogx" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11007792}}, adds the Publication Abstract to the page
+*[[Ketosteroid Isomerase|Ketosteroid Isomerase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11007792 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11007792}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-OGX 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 [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1e3n 1e3n]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGX OCA].
-==Reference==
-Detection of large pKa perturbations of an inhibitor and a catalytic group at an enzyme active site, a mechanistic basis for catalytic power of many enzymes., Ha NC, Kim MS, Lee W, Choi KY, Oh BH, J Biol Chem. 2000 Dec 29;275(52):41100-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11007792 11007792]
 [[Category: Pseudomonas putida]]
-[[Category: Single protein]]
+[[Category: Ha N-C]]
-[[Category: Steroid Delta-isomerase]]
+[[Category: Kim M-S]]
-[[Category: Ha, N C.]]
+[[Category: Oh B-H]]
-[[Category: Kim, M S.]]
-[[Category: Oh, B H.]]
-[[Category: Equilenin]]
-[[Category: Isomerase]]
-[[Category: Ketosteroid isomerase]]
-[[Category: Ksi]]
-[[Category: Lbhb]]
-[[Category: Pi]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 16:43:41 2008''