1zi9: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1zi9.png|left|200px]]
-<!--
+==Crystal Structure Analysis of the dienelactone hydrolase (E36D, C123S) mutant- 1.5 A==
-The line below this paragraph, containing "STRUCTURE_1zi9", creates the "Structure Box" on the page.
+<StructureSection load='1zi9' size='340' side='right'caption='[[1zi9]], [[Resolution|resolution]] 1.50&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'>[[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>
-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]] 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>
-{{STRUCTURE_1zi9|  PDB=1zi9  |  SCENE=  }}
+<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.
-===Crystal Structure Analysis of the dienelactone hydrolase (E36D, C123S) mutant- 1.5 A===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_15983415}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1zi9" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15983415 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15983415}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-ZI9 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=1ZI9 OCA].
-==Reference==
-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://www.ncbi.nlm.nih.gov/pubmed/15983415 15983415]
-[[Category: Carboxymethylenebutenolidase]]
 [[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: 3-d structure]]
-[[Category: Alpha and beta protein]]
-[[Category: Aromatic hydrocarbon]]
-[[Category: Catabolism]]
-[[Category: Hydrolase]]
-[[Category: Plasmid]]
-[[Category: Serine esterase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:40:19 2008''