5y02 - Revision history

OCA at 08:18, 22 November 2023

2023-11-22T08:18:18Z

←Older revision		Revision as of 08:18, 22 November 2023
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	==C-terminal peptide depleted mutant of hydroxynitrile lyase from Passiflora edulis (PeHNL) bound with (R)-mandelonitrile==		==C-terminal peptide depleted mutant of hydroxynitrile lyase from Passiflora edulis (PeHNL) bound with (R)-mandelonitrile==
-	<StructureSection load='5y02' size='340' side='right' caption='[[5y02]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5y02' size='340' side='right'caption='[[5y02]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y02]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pased Pased~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y02 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y02 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y02]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Passiflora_edulis Passiflora edulis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y02 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y02 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HBX:BENZALDEHYDE'>HBX</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=MXN:(2R)-HYDROXY(PHENYL)ETHANENITRILE'>MXN</scene>~~</td></tr>~~	+	</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xzq\|5xzq]], [[5xzt\|5xzt]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HBX:BENZALDEHYDE'>HBX</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=MXN:(2R)-HYDROXY(PHENYL)ETHANENITRILE'>MXN</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PeHNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=78168 PASED])~~</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=5y02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y02 OCA], [https://pdbe.org/5y02 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y02 RCSB], [https://www.ebi.ac.uk/pdbsum/5y02 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y02 ProSAT]</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=5y02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y02 OCA], [~~http~~://pdbe.org/5y02 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y02 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y02 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y02 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1L7NZN4_PASED A0A1L7NZN4_PASED]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pased~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Asano, Y~~]]	+	[[Category: Passiflora edulis]]
-	[[Category: ~~Motojima, F~~]]	+	[[Category: Asano Y]]
-	[[Category: ~~Nuylert, A~~]]	+	[[Category: Motojima F]]
-	[[Category: ~~Cyanohydrin]]~~	+	[[Category: Nuylert A]]
-	~~[[Category: Hydroxynitrile lyase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 07:37, 13 December 2017

2017-12-13T07:37:01Z

←Older revision		Revision as of 07:37, 13 December 2017
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	<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=5y02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y02 OCA], [http://pdbe.org/5y02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y02 RCSB], [http://www.ebi.ac.uk/pdbsum/5y02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y02 ProSAT]</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=5y02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y02 OCA], [http://pdbe.org/5y02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y02 RCSB], [http://www.ebi.ac.uk/pdbsum/5y02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y02 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hydroxynitrile lyases (HNLs) are enzymes used in the synthesis of chiral cyanohydrins. The HNL from Passiflora edulis (PeHNL) is R-selective and is the smallest HNL known to date. The crystal structures of PeHNL and its C-terminal peptide depleted derivative were determined by molecular replacement method using the template structure of a heat stable protein, SP1, from Populus tremula at 2.8 and 1.8 A resolution, respectively. PeHNL belongs to dimeric alpha+beta barrel superfamily consisting of a central beta-barrel in the middle of a dimer. The structure of PeHNL complexed with (R)-mandelonitrile ((R)-MAN) was also determined. The hydroxyl group of (R)-MAN forms hydrogen bonds with His8 and Tyr30 in the active site, whereas the nitrile group is oriented toward the carboxyl group of Glu54, unlike other HNLs, where it interacts with basic residues typically. The results of mutational analysis indicate that the catalytic dyad of His8-Asn101 is critical for the enzymatic reaction. The length of the hydrogen bond between His-Ndelta1 and Asn101-Odelta1 is short in the PeHNL-(R)-MAN complex (~ 2.6 A), which would increase the basicity of His8 to abstract a proton from the hydroxyl group of (R)-MAN. The cyanide ion released from the nitrile group abstracts a proton from the protonated His8 to generate a hydrogen cyanide. Thus, the His8 in the active site of PeHNL acts both as a general acid and a general base in the reaction. ENZYMES: EC 4.1.2.10 DATABASE: Structural data are available in PDB database under the accession numbers 5XZQ, 5XZT, and 5Y02.
		+
		+	The crystal structure and catalytic mechanism of hydroxynitrile lyase from passion fruit, Passiflora edulis.,Motojima F, Nuylert A, Asano Y FEBS J. 2017 Nov 20. doi: 10.1111/febs.14339. PMID:29155493<ref>PMID:29155493</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5y02" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:42, 29 November 2017

2017-11-29T07:42:03Z

←Older revision		Revision as of 07:42, 29 November 2017
Line 3:		Line 3:
	<StructureSection load='5y02' size='340' side='right' caption='[[5y02]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5y02' size='340' side='right' caption='[[5y02]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y02]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y02 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y02]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Pased Pased]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y02 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HBX:BENZALDEHYDE'>HBX</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=MXN:(2R)-HYDROXY(PHENYL)ETHANENITRILE'>MXN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HBX:BENZALDEHYDE'>HBX</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=MXN:(2R)-HYDROXY(PHENYL)ETHANENITRILE'>MXN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xzq\|5xzq]], [[5xzt\|5xzt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xzq\|5xzq]], [[5xzt\|5xzt]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PeHNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=78168 PASED])</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=5y02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y02 OCA], [http://pdbe.org/5y02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y02 RCSB], [http://www.ebi.ac.uk/pdbsum/5y02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y02 ProSAT]</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=5y02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y02 OCA], [http://pdbe.org/5y02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y02 RCSB], [http://www.ebi.ac.uk/pdbsum/5y02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y02 ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pased]]
	[[Category: Asano, Y]]		[[Category: Asano, Y]]
	[[Category: Motojima, F]]		[[Category: Motojima, F]]

OCA at 07:46, 22 November 2017

2017-11-22T07:46:10Z

←Older revision		Revision as of 07:46, 22 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5y02 is ON HOLD until Paper Publication~~	+	==C-terminal peptide depleted mutant of hydroxynitrile lyase from Passiflora edulis (PeHNL) bound with (R)-mandelonitrile==
-		+	<StructureSection load='5y02' size='340' side='right' caption='[[5y02]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors: Motojima, F., Nuylert, A., Asano, Y.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5y02]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y02 FirstGlance]. <br>
-	~~Description:~~ C-terminal peptide depleted mutant of hydroxynitrile lyase from Passiflora edulis (PeHNL) bound with (R)-mandelonitrile	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HBX:BENZALDEHYDE'>HBX</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=MXN:(2R)-HYDROXY(PHENYL)ETHANENITRILE'>MXN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xzq\|5xzq]], [[5xzt\|5xzt]]</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=5y02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y02 OCA], [http://pdbe.org/5y02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y02 RCSB], [http://www.ebi.ac.uk/pdbsum/5y02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y02 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Asano, Y]]
	[[Category: Motojima, F]]		[[Category: Motojima, F]]
	[[Category: Nuylert, A]]		[[Category: Nuylert, A]]
-	[[Category: ~~Asano, Y~~]]	+	[[Category: Cyanohydrin]]
		+	[[Category: Hydroxynitrile lyase]]
		+	[[Category: Lyase]]

OCA: Protected "5y02" [edit=sysop:move=sysop]

2017-09-27T15:59:13Z

Protected "5y02" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:59, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y02 is ON HOLD until Paper Publication Authors: Motojima, F., Nuylert, A., Asano, Y. Description: C-terminal peptide depleted mutant of hydroxynit...

2017-09-27T15:59:12Z

New page: '''Unreleased structure''' The entry 5y02 is ON HOLD until Paper Publication Authors: Motojima, F., Nuylert, A., Asano, Y. Description: C-terminal peptide depleted mutant of hydroxynit...

New page

'''Unreleased structure'''

The entry 5y02 is ON HOLD until Paper Publication

Authors: Motojima, F., Nuylert, A., Asano, Y.

Description: C-terminal peptide depleted mutant of hydroxynitrile lyase from Passiflora edulis (PeHNL) bound with (R)-mandelonitrile
[[Category: Unreleased Structures]]
[[Category: Motojima, F]]
[[Category: Nuylert, A]]
[[Category: Asano, Y]]