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1sck

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Revision as of 06:28, 10 November 2021

K236L mutant of hydroxynitrile lyase from Hevea brasiliensis in complex with acetone

Structural highlights

1sck is a 1 chain structure with sequence from Hevbr. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1qj4, 1yas, 2yas, 3yas, 4yas, 5yas, 6yas, 7yas, 1sc9, 1sci, 1scq
Gene:	HNL (HEVBR)
Activity:	Lyase, with EC number and 4.1.2.47 4.1.2.46 and 4.1.2.47
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The 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

↑ Gruber K, Gartler G, Krammer B, Schwab H, Kratky C. 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. J Biol Chem. 2004 May 7;279(19):20501-10. Epub 2004 Mar 3. PMID:14998991 doi:http://dx.doi.org/10.1074/jbc.M401575200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1sck"

@@ Line 3: / Line 3: @@
 <StructureSection load='1sck' size='340' side='right'caption='[[1sck]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1sck]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hevbr Hevbr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SCK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1SCK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1sck]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hevbr Hevbr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SCK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SCK FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACN:ACETONE'>ACN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qj4|1qj4]], [[1yas|1yas]], [[2yas|2yas]], [[3yas|3yas]], [[4yas|4yas]], [[5yas|5yas]], [[6yas|6yas]], [[7yas|7yas]], [[1sc9|1sc9]], [[1sci|1sci]], [[1scq|1scq]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 HEVBR])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HNL ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 HEVBR])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.46 and 4.1.2.47 4.1.2.46 and 4.1.2.47] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lyase Lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.46 and 4.1.2.47 4.1.2.46 and 4.1.2.47] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1sck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sck OCA], [http://pdbe.org/1sck PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sck RCSB], [http://www.ebi.ac.uk/pdbsum/1sck PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sck ProSAT]</span></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=1sck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sck OCA], [https://pdbe.org/1sck PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sck RCSB], [https://www.ebi.ac.uk/pdbsum/1sck PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sck ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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.
+[[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 ==
 [[Image:Consurf_key_small.gif|200px|right]]

1sck

From Proteopedia

Revision as of 06:28, 10 November 2021

K236L mutant of hydroxynitrile lyase from Hevea brasiliensis in complex with acetone

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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