1sc9

From Proteopedia

(Difference between revisions)

Revision as of 19:42, 10 September 2015

Hydroxynitrile Lyase from Hevea brasiliensis in complex with the natural substrate acetone cyanohydrin

Structural highlights

1sc9 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, 1sci, 1sck, 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

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/1sc9"

@@ Line 2: / Line 2: @@
 <StructureSection load='1sc9' size='340' side='right' caption='[[1sc9]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1sc9]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SC9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1sc9]] 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=1SC9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SC9 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CNH:2-HYDROXY-2-METHYLPROPANENITRILE'>CNH</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">[[1qj4|1qj4]], [[1yas|1yas]], [[2yas|2yas]], [[3yas|3yas]], [[4yas|4yas]], [[5yas|5yas]], [[6yas|6yas]], [[7yas|7yas]], [[1sci|1sci]], [[1sck|1sck]], [[1scq|1scq]]</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 Hevea brasiliensis])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydroxynitrilase Hydroxynitrilase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.37 4.1.2.37] </span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sc9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sc9 RCSB], [http://www.ebi.ac.uk/pdbsum/1sc9 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sc9 OCA], [http://pdbe.org/1sc9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sc9 RCSB], [http://www.ebi.ac.uk/pdbsum/1sc9 PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 29: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1sc9" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Hevea brasiliensis]]
+[[Category: Hevbr]]
-[[Category: Hydroxynitrilase]]
+[[Category: Lyase]]
 [[Category: Gartler, G]]
 [[Category: Gruber, K]]
@@ Line 42: / Line 43: @@
 [[Category: Alpha-beta hydrolase fold]]
 [[Category: Catalytic triad]]
-[[Category: Lyase]]
 [[Category: Substrate complex]]

1sc9

From Proteopedia

Revision as of 19:42, 10 September 2015

Hydroxynitrile Lyase from Hevea brasiliensis in complex with the natural substrate acetone cyanohydrin

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox