1zi9: Difference between revisions
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==Crystal Structure Analysis of the dienelactone hydrolase (E36D, C123S) mutant- 1.5 A== | ==Crystal Structure Analysis of the dienelactone hydrolase (E36D, C123S) mutant- 1.5 A== | ||
<StructureSection load='1zi9' size='340' side='right' caption='[[1zi9]], [[Resolution|resolution]] 1.50Å' scene=''> | <StructureSection load='1zi9' size='340' side='right'caption='[[1zi9]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1zi9]] is a 1 chain structure with sequence from [ | <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=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</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=' | <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> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/CLCD_PSEPU CLCD_PSEPU] Ring cleavage of cyclic ester dienelactone to produce maleylacetate. | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zi/1zi9_consurf.spt"</scriptWhenChecked> | <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> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
| Line 35: | Line 33: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Pseudomonas putida]] | ||
[[Category: Carr | [[Category: Carr PD]] | ||
[[Category: Kim | [[Category: Kim H-K]] | ||
[[Category: Liu | [[Category: Liu J-W]] | ||
[[Category: Ollis | [[Category: Ollis DL]] | ||
Latest revision as of 11:14, 25 October 2023
Crystal Structure Analysis of the dienelactone hydrolase (E36D, C123S) mutant- 1.5 ACrystal Structure Analysis of the dienelactone hydrolase (E36D, C123S) mutant- 1.5 A
Structural highlights
FunctionCLCD_PSEPU Ring cleavage of cyclic ester dienelactone to produce maleylacetate. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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