1w02: Difference between revisions

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-{{Seed}}
-[[Image:1w02.png|left|200px]]
-<!--
+==Crystal structure of mutant enzyme Y16F/D103L of ketosteroid isomerase from Pseudomonas putida biotype B==
-The line below this paragraph, containing "STRUCTURE_1w02", creates the "Structure Box" on the page.
+<StructureSection load='1w02' size='340' side='right'caption='[[1w02]], [[Resolution|resolution]] 2.30&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'>[[1w02]] is a 1 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=1W02 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W02 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]] 2.3&#8491;</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=1w02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w02 OCA], [https://pdbe.org/1w02 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w02 RCSB], [https://www.ebi.ac.uk/pdbsum/1w02 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w02 ProSAT]</span></td></tr>
-{{STRUCTURE_1w02|  PDB=1w02  |  SCENE=  }}
+</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/w0/1w02_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=1w02 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+KSI (ketosteroid isomerase) catalyses an allylic isomerization reaction at a diffusion-controlled rate. A hydrogen bond network, Asp(99).Water(504).Tyr(14).Tyr(55).Tyr(30), connects two critical catalytic residues, Tyr(14) and Asp(99), with Tyr(30), Tyr(55) and a water molecule in the highly apolar active site of the Pseudomonas putida KSI. In order to characterize the interactions among these amino acids in the hydrogen bond network of KSI, double-mutant cycle analysis was performed, and the crystal structure of each mutant protein within the cycle was determined respectively to interpret the coupling energy. The DeltaDeltaG(o) values of Y14F/D99L (Tyr(14)--&gt;Phe/Asp(99)--&gt;Leu) KSI, 25.5 kJ/mol for catalysis and 28.9 kJ/mol for stability, were smaller than the sums (i.e. 29.7 kJ/mol for catalysis and 34.3 kJ/mol for stability) for single mutant KSIs respectively, indicating that the effect of the Y14F/D99L mutation was partially additive for both catalysis and stability. The partially additive effect of the Y14F/D99L mutation suggests that Tyr(14) and Asp(99) should interact positively for the stabilization of the transition state during the catalysis. The crystal structure of Y14F/D99L KSI indicated that the Y14F/D99L mutation increased the hydrophobic interaction while disrupting the hydrogen bond network. The DeltaDeltaG(o) values of both Y30F/D99L and Y55F/D99L KSIs for the catalysis and stability were larger than the sum of single mutants, suggesting that either Tyr(30) and Asp(99) or Tyr(55) and Asp(99) should interact negatively for the catalysis and stability. These synergistic effects of both Y30F/D99L and Y55F/D99L mutations resulted from the disruption of the hydrogen bond network. The synergistic effect of the Y55F/D99L mutation was larger than that of the Y30F/D99L mutation, since the former mutation impaired the proper positioning of a critical catalytic residue, Tyr(14), involved in the catalysis of KSI. The present study can provide insight into interpreting the coupling energy measured by double-mutant cycle analysis based on the crystal structures of the wild-type and mutant proteins.
-===CRYSTAL STRUCTURE OF MUTANT ENZYME Y16F/D103L OF KETOSTEROID ISOMERASE FROM PSEUDOMONAS PUTIDA BIOTYPE B===
+Structural double-mutant cycle analysis of a hydrogen bond network in ketosteroid isomerase from Pseudomonas putida biotype B.,Jang DS, Cha HJ, Cha SS, Hong BH, Ha NC, Lee JY, Oh BH, Lee HS, Choi KY Biochem J. 2004 Sep 15;382(Pt 3):967-73. PMID:15228388<ref>PMID:15228388</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1w02" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15228388}}, adds the Publication Abstract to the page
+*[[Ketosteroid Isomerase|Ketosteroid Isomerase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15228388 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15228388}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-W02 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=1W02 OCA].
-==Reference==
-Structural double-mutant cycle analysis of a hydrogen bond network in ketosteroid isomerase from Pseudomonas putida biotype B., Jang DS, Cha HJ, Cha SS, Hong BH, Ha NC, Lee JY, Oh BH, Lee HS, Choi KY, Biochem J. 2004 Sep 15;382(Pt 3):967-73. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15228388 15228388]
 [[Category: Pseudomonas putida]]
-[[Category: Single protein]]
+[[Category: Choi KY]]
-[[Category: Steroid Delta-isomerase]]
+[[Category: Jang DS]]
-[[Category: Cha, H J.]]
-[[Category: Choi, K Y.]]
-[[Category: Jang, D S.]]
-[[Category: Closed barrel]]
-[[Category: Coneshell]]
-[[Category: Curved b-sheet]]
-[[Category: Isomerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 08:53:20 2008''