1e3v: Difference between revisions

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-[[Image:1e3v.jpg|left|200px]]
- {{Structure
+==Crystal structure of ketosteroid isomerase from Psedomonas putida complexed with deoxycholate==
-|PDB= 1e3v |SIZE=350|CAPTION= <scene name='initialview01'>1e3v</scene>, resolution 2.0&Aring;
+<StructureSection load='1e3v' size='340' side='right'caption='[[1e3v]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DXC:(3ALPHA,5ALPHA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC+ACID'>DXC</scene>
+<table><tr><td colspan='2'>[[1e3v]] is a 2 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=1E3V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E3V FirstGlance]. <br>
-|ACTIVITY=
+</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>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DXC:(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC+ACID'>DXC</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=1e3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e3v OCA], [https://pdbe.org/1e3v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e3v RCSB], [https://www.ebi.ac.uk/pdbsum/1e3v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e3v ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1e3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e3v OCA], [http://www.ebi.ac.uk/pdbsum/1e3v PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1e3v 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/e3/1e3v_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=1e3v 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.
-'''CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE FROM PSEDOMONAS PUTIDA COMPLEXED WITH DEOXYCHOLATE'''
+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 1e3v" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-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.
+*[[Ketosteroid Isomerase|Ketosteroid Isomerase]]
+== References ==
-==About this Structure==
+<references/>
-E3V is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E3V OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-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: Ha, N C.]]
+[[Category: Kim J-S]]
-[[Category: Kim, J S.]]
+[[Category: Kim M-S]]
-[[Category: Kim, M S.]]
+[[Category: Oh B-H]]
-[[Category: Oh, B H.]]
-[[Category: deoxychlate]]
-[[Category: ksi]]
-[[Category: lbhb]]
-[[Category: reverse binding]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:54:37 2008''