1zi9: Difference between revisions

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OCA

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-[[Image:1zi9.gif|left|200px]]<br /><applet load="1zi9" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1zi9, resolution 1.50&Aring;" />
-'''Crystal Structure Analysis of the dienelactone hydrolase (E36D, C123S) mutant- 1.5 A'''<br />
-==Overview==
+==Crystal Structure Analysis of the dienelactone hydrolase (E36D, C123S) mutant- 1.5 A==
-The enzyme dienelactone hydrolase (DLH) has undergone directed evolution, to produce a series of mutant proteins that have enhanced activity towards, the non-physiological substrates alpha-naphthyl acetate and p-nitrophenyl, acetate. In terms of steady-state kinetics, the mutations caused a drop in, the K(m) for the hydrolysis reaction with these two substrates. For the, best mutant, there was a 5.6-fold increase in k(cat)/K(m) for the, hydrolysis of alpha-naphthyl acetate and a 3.6-fold increase was observed, for p-nitrophenyl acetate. For alpha-naphthyl acetate the pre-steady-state, kinetics revealed that the rate constant for the formation of the covalent, intermediate had increased. The mutations responsible for the rate, enhancements map to the active site. The structures of the starting and, mutated proteins revealed small changes in the protein owing to the, mutations, while the structures of the same proteins with an inhibitor, co-crystallized in the active site indicated that the mutations caused, significant changes in the way the mutated proteins recognized the, substrates. Within the active site of the mutant proteins, the inhibitor, was rotated by about 180 degrees with respect to the orientation found in, the starting enzyme. This rotation of the inhibitor caused the, displacement of a large section of a loop on one side of the active site., Residues that could stabilize the transition state for the reaction were, identified.
+<StructureSection load='1zi9' size='340' side='right'caption='[[1zi9]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1zi9]] 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=1ZI9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZI9 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1zi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zi9 OCA], [https://pdbe.org/1zi9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zi9 RCSB], [https://www.ebi.ac.uk/pdbsum/1zi9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zi9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CLCD_PSEPU CLCD_PSEPU] Ring cleavage of cyclic ester dienelactone to produce maleylacetate.
+== 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/zi/1zi9_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=1zi9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The enzyme dienelactone hydrolase (DLH) has undergone directed evolution to produce a series of mutant proteins that have enhanced activity towards the non-physiological substrates alpha-naphthyl acetate and p-nitrophenyl acetate. In terms of steady-state kinetics, the mutations caused a drop in the K(m) for the hydrolysis reaction with these two substrates. For the best mutant, there was a 5.6-fold increase in k(cat)/K(m) for the hydrolysis of alpha-naphthyl acetate and a 3.6-fold increase was observed for p-nitrophenyl acetate. For alpha-naphthyl acetate the pre-steady-state kinetics revealed that the rate constant for the formation of the covalent intermediate had increased. The mutations responsible for the rate enhancements map to the active site. The structures of the starting and mutated proteins revealed small changes in the protein owing to the mutations, while the structures of the same proteins with an inhibitor co-crystallized in the active site indicated that the mutations caused significant changes in the way the mutated proteins recognized the substrates. Within the active site of the mutant proteins, the inhibitor was rotated by about 180 degrees with respect to the orientation found in the starting enzyme. This rotation of the inhibitor caused the displacement of a large section of a loop on one side of the active site. Residues that could stabilize the transition state for the reaction were identified.
-==About this Structure==
+Following directed evolution with crystallography: structural changes observed in changing the substrate specificity of dienelactone hydrolase.,Kim HK, Liu JW, Carr PD, Ollis DL Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):920-31. Epub 2005, Jun 24. PMID:15983415<ref>PMID:15983415</ref>
-ZI9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with SO4 and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Carboxymethylenebutenolidase Carboxymethylenebutenolidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.45 3.1.1.45] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ZI9 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Following directed evolution with crystallography: structural changes observed in changing the substrate specificity of dienelactone hydrolase., Kim HK, Liu JW, Carr PD, Ollis DL, Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):920-31. Epub 2005, Jun 24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15983415 15983415]
+</div>
-[[Category: Carboxymethylenebutenolidase]]
+<div class="pdbe-citations 1zi9" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Pseudomonas putida]]
-[[Category: Single protein]]
+[[Category: Carr PD]]
-[[Category: Carr, P.D.]]
+[[Category: Kim H-K]]
-[[Category: Kim, H.K.]]
+[[Category: Liu J-W]]
-[[Category: Liu, J.W.]]
+[[Category: Ollis DL]]
-[[Category: Ollis, D.L.]]
-[[Category: GOL]]
-[[Category: SO4]]
-[[Category: 3-d structure]]
-[[Category: alpha and beta proteins]]
-[[Category: aromatic hydrocarbons]]
-[[Category: catabolism]]
-[[Category: hydrolase]]
-[[Category: plasmid]]
-[[Category: serine esterase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:28:15 2007''