1yb6: Difference between revisions

Revision as of 17:03, 21 February 2008

Hydroxynitrile lyase from hevea brasiliensis in complex with mandelonitrile

OverviewOverview

The hydroxynitrile lyase from the tropical rubber tree Hevea brasiliensis (HbHNL) is utilized as a biocatalyst in stereospecific syntheses of alpha-hydroxynitriles from aldehydes and methyl-ketones. The catalyzed reaction represents one of the few industrially relevant examples of enzyme mediated C-C coupling reactions. In this work, we determined the X-ray crystal structures (at 1.54 and 1.76 Angstroms resolution) of HbHNL complexes with two chiral substrates -- mandelonitrile and 2,3-dimethyl-2-hydroxy-butyronitrile -- by soaking and rapid freeze quenching techniques. This is the first structural observation of the complex between a HNL and chiral substrates. Consistent with the known selectivity of the enzyme, only the S-enantiomers of the two substrates were observed in the active site. The binding modes of the chiral substrates were identical to that observed for the biological substrate acetone cyanohydrin. This indicates that the transformation of these non-natural substrates follows the same mechanism. A large hydrophobic pocket was identified in the active site of HbHNL which accommodates the more voluminous substituents of the two substrates. A three-point binding mode of the substrates -- hydrophobic pocket, hydrogen bonds between the hydroxyl group and Ser80 and Thr11, electrostatic interaction of the cyano group with Lys236 -- offers a likely structural explanation for the enantioselectivity of the enzyme. The structural data rationalize the observed (S)-enantioselectivity and form the basis for modifying the stereospecificity through rational design. The structures also revealed the necessity of considerable flexibility of the sidechain of Trp128 in order to bind and transform larger substrates.

About this StructureAbout this Structure

1YB6 is a Single protein structure of sequence from Hevea brasiliensis with and as ligands. Active as Transfered to EC 4.1.2.37, with EC number 4.1.2.39 Full crystallographic information is available from OCA.

ReferenceReference

Structural determinants of the enantioselectivity of the hydroxynitrile lyase from Hevea brasiliensis., Gartler G, Kratky C, Gruber K, J Biotechnol. 2007 Mar 30;129(1):87-97. Epub 2006 Dec 17. PMID:17250917

Page seeded by OCA on Thu Feb 21 16:03:32 2008

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-[[Image:1yb6.gif|left|200px]]<br /><applet load="1yb6" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1yb6.gif|left|200px]]<br /><applet load="1yb6" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1yb6, resolution 1.54&Aring;" />
 '''Hydroxynitrile lyase from hevea brasiliensis in complex with mandelonitrile'''<br />
 ==Overview==
-The hydroxynitrile lyase from the tropical rubber tree Hevea brasiliensis, (HbHNL) is utilized as a biocatalyst in stereospecific syntheses of, alpha-hydroxynitriles from aldehydes and methyl-ketones. The catalyzed, reaction represents one of the few industrially relevant examples of, enzyme mediated C-C coupling reactions. In this work, we determined the, X-ray crystal structures (at 1.54 and 1.76A resolution) of HbHNL complexes, with two chiral substrates - mandelonitrile and, 2,3-dimethyl-2-hydroxy-butyronitrile - by soaking and rapid freeze, quenching techniques. This is the first structural observation of the, complex between a HNL and chiral substrates. Consistent with the known, selectivity of the enzyme, only the S-enantiomers of the two substrates, were observed in the active site. The binding modes of the chiral, substrates were identical to that observed for the biological substrate, acetone cyanohydrin. This indicates that the transformation of these, non-natural substrates follows the same mechanism. A large hydrophobic, pocket was identified in the active site of HbHNL which accommodates the, more voluminous substituents of the two substrates. A three-point binding, mode of the substrates - hydrophobic pocket, hydrogen bonds between the, hydroxyl group and Ser80 and Thr11, electrostatic interaction of the cyano, group with Lys236 - offers a likely structural explanation for the, enantioselectivity of the enzyme. The structural data rationalize the, observed (S)-enantioselectivity and form the basis for modifying the, stereospecificity through rational design. The structures also revealed, the necessity of considerable flexibility of the sidechain of Trp128 in, order to bind and transform larger substrates.
+The hydroxynitrile lyase from the tropical rubber tree Hevea brasiliensis (HbHNL) is utilized as a biocatalyst in stereospecific syntheses of alpha-hydroxynitriles from aldehydes and methyl-ketones. The catalyzed reaction represents one of the few industrially relevant examples of enzyme mediated C-C coupling reactions. In this work, we determined the X-ray crystal structures (at 1.54 and 1.76 Angstroms resolution) of HbHNL complexes with two chiral substrates -- mandelonitrile and 2,3-dimethyl-2-hydroxy-butyronitrile -- by soaking and rapid freeze quenching techniques. This is the first structural observation of the complex between a HNL and chiral substrates. Consistent with the known selectivity of the enzyme, only the S-enantiomers of the two substrates were observed in the active site. The binding modes of the chiral substrates were identical to that observed for the biological substrate acetone cyanohydrin. This indicates that the transformation of these non-natural substrates follows the same mechanism. A large hydrophobic pocket was identified in the active site of HbHNL which accommodates the more voluminous substituents of the two substrates. A three-point binding mode of the substrates -- hydrophobic pocket, hydrogen bonds between the hydroxyl group and Ser80 and Thr11, electrostatic interaction of the cyano group with Lys236 -- offers a likely structural explanation for the enantioselectivity of the enzyme. The structural data rationalize the observed (S)-enantioselectivity and form the basis for modifying the stereospecificity through rational design. The structures also revealed the necessity of considerable flexibility of the sidechain of Trp128 in order to bind and transform larger substrates.
 ==About this Structure==
-YB6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis] with SO4 and MNN as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Transfered_to_EC_4.1.2.37 Transfered to EC 4.1.2.37], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.39 4.1.2.39] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YB6 OCA].
+YB6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=MNN:'>MNN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Transfered_to_EC_4.1.2.37 Transfered to EC 4.1.2.37], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.39 4.1.2.39] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB6 OCA].
 ==Reference==
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 [[Category: Hevea brasiliensis]]
 [[Category: Single protein]]
-[[Category: Transfered to EC 4.1.2.37]]
+[[Category: Transfered to EC 4 1.2 37]]
 [[Category: Gartler, G.]]
 [[Category: Gruber, K.]]
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 [[Category: alpha-beta hydrolase fold; substrate complex; catalytic triad]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:39:48 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:03:32 2008''