1sc9: Difference between revisions
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==Hydroxynitrile Lyase from Hevea brasiliensis in complex with the natural substrate acetone cyanohydrin== | ==Hydroxynitrile Lyase from Hevea brasiliensis in complex with the natural substrate acetone cyanohydrin== | ||
<StructureSection load='1sc9' size='340' side='right' caption='[[1sc9]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='1sc9' size='340' side='right'caption='[[1sc9]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1sc9]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1sc9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SC9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SC9 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]] 1.8Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CNH:2-HYDROXY-2-METHYLPROPANENITRILE'>CNH</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=1sc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sc9 OCA], [https://pdbe.org/1sc9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sc9 RCSB], [https://www.ebi.ac.uk/pdbsum/1sc9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sc9 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/HNL_HEVBR HNL_HEVBR] Involved in cyanogenesis, the release of HCN from injured tissues. Decomposes a varieties of (R) or (S) cyanohydrins into HCN and the corresponding aldehydes and ketones. The natural substrate of this enzyme is (S)-acetone cyanohydrin. | ||
== 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/sc/1sc9_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sc/1sc9_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> | ||
</jmolCheckbox> | </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/ | </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=1sc9 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 1sc9" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 34: | Line 34: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Hevea brasiliensis]] | [[Category: Hevea brasiliensis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Gartler | [[Category: Gartler G]] | ||
[[Category: Gruber | [[Category: Gruber K]] | ||
[[Category: Krammer | [[Category: Krammer B]] | ||
[[Category: Kratky | [[Category: Kratky C]] | ||
[[Category: Schwab | [[Category: Schwab H]] | ||
Latest revision as of 10:25, 25 October 2023
Hydroxynitrile Lyase from Hevea brasiliensis in complex with the natural substrate acetone cyanohydrinHydroxynitrile Lyase from Hevea brasiliensis in complex with the natural substrate acetone cyanohydrin
Structural highlights
FunctionHNL_HEVBR Involved in cyanogenesis, the release of HCN from injured tissues. Decomposes a varieties of (R) or (S) cyanohydrins into HCN and the corresponding aldehydes and ketones. The natural substrate of this enzyme is (S)-acetone cyanohydrin. 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 hydroxynitrile lyases (HNLs) from Hevea brasiliensis (HbHNL) and from Manihot esculenta (MeHNL) are both members of the alpha/beta-hydrolase superfamily. Mechanistic proposals have been put forward in the past for both enzymes; they differed with respect to the role of the active-site lysine residue for which a catalytic function was claimed for the Hevea enzyme but denied for the Manihot enzyme. We applied a freeze-quench method to prepare crystals of the complex of HbHNL with the biological substrate acetone cyanohydrin and determined its three-dimensional structure. Site-directed mutagenesis was used to prepare the mutant K236L, which is inactive although its three-dimensional structure is similar to the wild-type enzyme. However, the structure of the K236L-acetone cyanohydrin complex shows the substrate in a different orientation from the wild-type complex. Finite difference Poisson-Boltzmann calculations show that in the absence of Lys(236) the catalytic base His(235) would be protonated at neutral pH. All of this suggests that Lys(236) is instrumental for catalysis in several ways, i.e. by correctly positioning the substrate, by stabilizing the negatively charged reaction product CN(-), and by modulating the basicity of the catalytic base. These data complete the elucidation of the reaction mechanism of alpha/beta-hydrolase HNLs, in which the catalytic triad acts as a general base rather than as a nucleophile; proton abstraction from the substrate is performed by the serine, and reprotonation of the product cyanide is performed by the histidine residues. Together with a threonine side chain, the active-site serine and lysine are also involved in substrate binding. Reaction mechanism of hydroxynitrile lyases of the alpha/beta-hydrolase superfamily: the three-dimensional structure of the transient enzyme-substrate complex certifies the crucial role of LYS236.,Gruber K, Gartler G, Krammer B, Schwab H, Kratky C J Biol Chem. 2004 May 7;279(19):20501-10. Epub 2004 Mar 3. PMID:14998991[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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