7vb3 - Revision history

OCA at 09:16, 17 October 2024

2024-10-17T09:16:39Z

← Older revision		Revision as of 09:16, 17 October 2024
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	<StructureSection load='7vb3' size='340' side='right'caption='[[7vb3]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='7vb3' size='340' side='right'caption='[[7vb3]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7vb3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Linum_usitatissimum Linum usitatissimum].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VB3 FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VB3 FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.48Å</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]] 1.48Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=7vb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vb3 OCA], [https://pdbe.org/7vb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vb3 RCSB], [https://www.ebi.ac.uk/pdbsum/7vb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vb3 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=7vb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vb3 OCA], [https://pdbe.org/7vb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vb3 RCSB], [https://www.ebi.ac.uk/pdbsum/7vb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vb3 ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[https://www.uniprot.org/uniprot/AHNL_LINUS AHNL_LINUS] Involved in the catabolism of cyanogenic glycosides. Naturally occurring substrates are the aliphatic acetone cyanohydrin and butan-2-one cyanohydrin, which are the aglycones of the cyanogenic glycosides linamarin, lotaustralin, linustatin and neolinustatin. Can use various aliphatic ketones and aldehydes as substrates, but not aromatic ketones.[REFERENCE:5]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Linum usitatissimum]]~~
	[[Category: Asano Y]]		[[Category: Asano Y]]
	[[Category: Nakabayashi M]]		[[Category: Nakabayashi M]]
	[[Category: Zheng D]]		[[Category: Zheng D]]

OCA at 17:22, 29 November 2023

2023-11-29T17:22:34Z

← Older revision		Revision as of 17:22, 29 November 2023
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	<StructureSection load='7vb3' size='340' side='right'caption='[[7vb3]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='7vb3' size='340' side='right'caption='[[7vb3]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7vb3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VB3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7vb3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Linum_usitatissimum Linum usitatissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VB3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.48Å</td></tr>
	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Aliphatic_(R)-hydroxynitrile_lyase Aliphatic (R)-hydroxynitrile lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.46 4.1.2.46]~~ </~~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=7vb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vb3 OCA], [https://pdbe.org/7vb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vb3 RCSB], [https://www.ebi.ac.uk/pdbsum/7vb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vb3 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=7vb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vb3 OCA], [https://pdbe.org/7vb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vb3 RCSB], [https://www.ebi.ac.uk/pdbsum/7vb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vb3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/AHNL_LINUS AHNL_LINUS]] Involved in the catabolism of cyanogenic glycosides. Naturally occurring substrates are the aliphatic acetone cyanohydrin and butan-2-one cyanohydrin, which are the aglycones of the cyanogenic glycosides linamarin, lotaustralin, linustatin and neolinustatin. Can use various aliphatic ketones and aldehydes as substrates, but not aromatic ketones.[REFERENCE:5]		[https://www.uniprot.org/uniprot/AHNL_LINUS AHNL_LINUS] Involved in the catabolism of cyanogenic glycosides. Naturally occurring substrates are the aliphatic acetone cyanohydrin and butan-2-one cyanohydrin, which are the aglycones of the cyanogenic glycosides linamarin, lotaustralin, linustatin and neolinustatin. Can use various aliphatic ketones and aldehydes as substrates, but not aromatic ketones.[REFERENCE:5]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Asano, Y~~]]		[[Category: Linum usitatissimum]]
	[[Category: ~~Nakabayashi, M~~]]		[[Category: Asano Y]]
	[[Category: ~~Zheng, D~~]]		[[Category: Nakabayashi M]]
	[[Category: ~~Hydroxynitrile lyase]]~~		[[Category: Zheng D]]
	~~[[Category: Lyase]]~~
	~~[[Category: Nad~~]]

OCA at 07:25, 16 March 2022

2022-03-16T07:25:31Z

← Older revision		Revision as of 07:25, 16 March 2022
Line 1:		Line 1:

	==Crystal structure of hydroxynitrile lyase from Linum usitatissimum==		==Crystal structure of hydroxynitrile lyase from Linum usitatissimum==
	<StructureSection load='7vb3' size='340' side='right'caption='[[7vb3]]' scene=''>		<StructureSection load='7vb3' size='340' side='right'caption='[[7vb3]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VB3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7vb3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VB3 FirstGlance]. <br>
	</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=7vb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vb3 OCA], [https://pdbe.org/7vb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vb3 RCSB], [https://www.ebi.ac.uk/pdbsum/7vb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vb3 ProSAT]</span></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
			<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene></td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aliphatic_(R)-hydroxynitrile_lyase Aliphatic (R)-hydroxynitrile lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.46 4.1.2.46] </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=7vb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vb3 OCA], [https://pdbe.org/7vb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vb3 RCSB], [https://www.ebi.ac.uk/pdbsum/7vb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vb3 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[https://www.uniprot.org/uniprot/AHNL_LINUS AHNL_LINUS]] Involved in the catabolism of cyanogenic glycosides. Naturally occurring substrates are the aliphatic acetone cyanohydrin and butan-2-one cyanohydrin, which are the aglycones of the cyanogenic glycosides linamarin, lotaustralin, linustatin and neolinustatin. Can use various aliphatic ketones and aldehydes as substrates, but not aromatic ketones.[REFERENCE:5]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Hydroxynitrile lyase from Linum usitatissimum (LuHNL) is an enzyme involved in the catabolism of cyanogenic glycosides to release hydrogen cyanide upon tissue damage. This enzyme strictly conserves the substrate- and NAD(H)-binding domains of Zn2+-containing alcohol dehydrogenase (ADH); however, there is no evidence suggesting that LuHNL possesses ADH activity. Herein, we determined the ligand-free 3D structure of LuHNL and its complex with acetone cyanohydrin and (R)-2-butanone cyanohydrin using X-ray crystallography. These structures reveal that an A-form NAD+ is tightly but not covalently bound to each subunit of LuHNL. The restricted movement of the NAD+ molecule is due to the "sandwich-structure" on the adenine moiety of NAD+. Moreover, the structures and mutagenesis analysis reveal a novel reaction mechanism for cyanohydrin decomposition involving the cyano-zinc complex and hydrogen-bonded interaction of the hydroxyl group of cyanohydrin with Glu323/Thr65 and H2O/Lys162 of LuHNL. The deprotonated Lys162 and protonated Glu323 residues are presumably stabilized by a partially desolvated microenvironment. In summary, the substrate-binding geometry of LuHNL provides insights into the differences in activities of LuHNL and ADH, and identifying this novel reaction mechanism is an important contribution to the study of hydroxynitrile lyases.

			Structural characterization of Linum usitatissimum hydroxynitrile lyase: a new cyanohydrin decomposition mechanism involving a cyano-zinc complex.,Zheng D, Nakabayashi M, Asano Y J Biol Chem. 2022 Jan 28:101650. doi: 10.1016/j.jbc.2022.101650. PMID:35101448<ref>PMID:35101448</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7vb3" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Asano Y]]		[[Category: Asano, Y]]
	[[Category: Nakabayashi M]]		[[Category: Nakabayashi, M]]
	[[Category: Zheng D]]		[[Category: Zheng, D]]
			[[Category: Hydroxynitrile lyase]]
			[[Category: Lyase]]
			[[Category: Nad]]

OCA at 07:27, 9 February 2022

2022-02-09T07:27:07Z

← Older revision		Revision as of 07:27, 9 February 2022
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	~~'''Unreleased structure'''~~

	~~The entry~~ 7vb3 is ~~ON HOLD until Paper Publication~~		==Crystal structure of hydroxynitrile lyase from Linum usitatissimum==
			<StructureSection load='7vb3' size='340' side='right'caption='[[7vb3]]' scene=''>
	~~Authors~~: ~~Zheng~~, D., ~~Nakabayashi~~, M., ~~Asano~~, Y.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VB3 FirstGlance]. <br>
	~~Description: Crystal structure of hydroxynitrile lyase from Linum usitatissimum~~		</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=7vb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vb3 OCA], [https://pdbe.org/7vb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vb3 RCSB], [https://www.ebi.ac.uk/pdbsum/7vb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vb3 ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: Asano, Y]]		__TOC__
	[[Category: Nakabayashi, M]]		</StructureSection>
	[[Category: Zheng, D]]		[[Category: Large Structures]]
			[[Category: Asano Y]]
			[[Category: Nakabayashi M]]
			[[Category: Zheng D]]

OCA at 12:17, 29 December 2021

2021-12-29T12:17:41Z

← Older revision		Revision as of 12:17, 29 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7vb3 is ON HOLD		The entry 7vb3 is ON HOLD until Paper Publication

	Authors: Zheng, D., Nakabayashi, M., Asano, Y.		Authors: Zheng, D., Nakabayashi, M., Asano, Y.

OCA at 15:46, 15 December 2021

2021-12-15T15:46:11Z

← Older revision		Revision as of 15:46, 15 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7vb3 is ON HOLD ~~until Paper Publication~~		The entry 7vb3 is ON HOLD

	Authors: Zheng, D., Nakabayashi, M., Asano, Y.		Authors: Zheng, D., Nakabayashi, M., Asano, Y.

OCA at 08:25, 15 September 2021

2021-09-15T08:25:14Z

← Older revision		Revision as of 08:25, 15 September 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7vb3 is ON HOLD		The entry 7vb3 is ON HOLD until Paper Publication

	Authors: Zheng, D., Nakabayashi, M., Asano, Y.		Authors: Zheng, D., Nakabayashi, M., Asano, Y.

OCA: Protected "7vb3" [edit=sysop:move=sysop]

2021-09-08T08:02:19Z

Protected "7vb3" [edit=sysop:move=sysop]

← Older revision	Revision as of 08:02, 8 September 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7vb3 is ON HOLD Authors: Zheng, D., Nakabayashi, M., Asano, Y. Description: Crystal structure of hydroxynitrile lyase from Linum usitatissimum [[Ca...

2021-09-08T08:02:18Z

New page: '''Unreleased structure''' The entry 7vb3 is ON HOLD Authors: Zheng, D., Nakabayashi, M., Asano, Y. Description: Crystal structure of hydroxynitrile lyase from Linum usitatissimum [[Ca...

New page

'''Unreleased structure'''

The entry 7vb3 is ON HOLD

Authors: Zheng, D., Nakabayashi, M., Asano, Y.

Description: Crystal structure of hydroxynitrile lyase from Linum usitatissimum
[[Category: Unreleased Structures]]
[[Category: Asano, Y]]
[[Category: Nakabayashi, M]]
[[Category: Zheng, D]]