1yb6: Difference between revisions
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|PDB= 1yb6 |SIZE=350|CAPTION= <scene name='initialview01'>1yb6</scene>, resolution 1.54Å | |PDB= 1yb6 |SIZE=350|CAPTION= <scene name='initialview01'>1yb6</scene>, resolution 1.54Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=MNN:(S)-MANDELIC+ACID+NITRILE'>MNN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> | ||
|ACTIVITY= [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] | |ACTIVITY= <span class='plainlinks'>[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] </span> | ||
|GENE= HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 Hevea brasiliensis]) | |GENE= HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 Hevea brasiliensis]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1sc9|1SC9]], [[1sci|1SCI]], [[1sck|1SCK]], [[1scq|1SCQ]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yb6 OCA], [http://www.ebi.ac.uk/pdbsum/1yb6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yb6 RCSB]</span> | |||
}} | }} | ||
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[[Category: Gruber, K.]] | [[Category: Gruber, K.]] | ||
[[Category: Kratky, C.]] | [[Category: Kratky, C.]] | ||
[[Category: | [[Category: alpha-beta hydrolase fold]] | ||
[[Category: | [[Category: catalytic triad]] | ||
[[Category: | [[Category: substrate complex]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:01:27 2008'' | ||
Revision as of 01:01, 31 March 2008
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| , resolution 1.54Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | HNL (Hevea brasiliensis) | ||||||
| Activity: | Transfered to EC 4.1.2.37, with EC number 4.1.2.39 | ||||||
| Related: | 1SC9, 1SCI, 1SCK, 1SCQ
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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
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