5xem - Revision history

OCA at 06:47, 14 October 2020

2020-10-14T06:47:37Z

←Older revision		Revision as of 06:47, 14 October 2020
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	==Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-lanthionine-PLP Schiff base==		==Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-lanthionine-PLP Schiff base==
-	<StructureSection load='5xem' size='340' side='right' caption='[[5xem]], [[Resolution\|resolution]] 1.84Å' scene=''>	+	<StructureSection load='5xem' size='340' side='right'caption='[[5xem]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xem]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XEM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xem]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XEM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=85F:(2R)-2-azanyl-3-[(2R)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-propanoic+acid'>85F</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene>, <scene name='pdbligand=PG5:1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE'>PG5</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=85F:(2R)-2-azanyl-3-[(2R)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-propanoic+acid'>85F</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene>, <scene name='pdbligand=PG5:1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE'>PG5</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xeo\|5xeo]], [[5xen\|5xen]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xeo\|5xeo]], [[5xen\|5xen]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cysteine_synthase Cysteine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.47 2.5.1.47] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cysteine_synthase Cysteine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.47 2.5.1.47] </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=5xem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xem OCA], [http://pdbe.org/5xem PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xem RCSB], [http://www.ebi.ac.uk/pdbsum/5xem PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xem ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xem OCA], [http://pdbe.org/5xem PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xem RCSB], [http://www.ebi.ac.uk/pdbsum/5xem PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xem ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Cysteine synthase]]		[[Category: Cysteine synthase]]
		+	[[Category: Large Structures]]
	[[Category: Kezuka, Y]]		[[Category: Kezuka, Y]]
	[[Category: Nonaka, T]]		[[Category: Nonaka, T]]

OCA at 13:46, 11 April 2018

2018-04-11T13:46:47Z

←Older revision		Revision as of 13:46, 11 April 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5xem is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-lanthionine-PLP Schiff base==
		+	<StructureSection load='5xem' size='340' side='right' caption='[[5xem]], [[Resolution\|resolution]] 1.84Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xem]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XEM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=85F:(2R)-2-azanyl-3-[(2R)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-propanoic+acid'>85F</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene>, <scene name='pdbligand=PG5:1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE'>PG5</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xeo\|5xeo]], [[5xen\|5xen]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cysteine_synthase Cysteine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.47 2.5.1.47] </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=5xem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xem OCA], [http://pdbe.org/5xem PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xem RCSB], [http://www.ebi.ac.uk/pdbsum/5xem PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xem ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hydrogen sulfide produced by oral bacteria is responsible for oral malodour. Two homologous hydrogen sulfide-producing enzymes, Fn1220 and Cdl, from Fusobacterium nucleatum (which actively produces hydrogen sulfide) were overproduced, purified and crystallized. X-ray diffraction data were collected from the crystals using a synchrotron-radiation source. The Fn1220 crystal belonged to tetragonal space group P4(1)2(1)2 or P4(3)2(1)2 (unit-cell parameters a=b=116.8, c=99.2 A) and the Cdl crystal belonged to monoclinic space group P2(1) (unit-cell parameters a=84.9, b=70.9, c=87.6 A, beta=90.3 degrees ).

-	~~Authors: Kezuka~~, Y., ~~Yoshida~~, Y., Nonaka, T.	+	Purification, crystallization and preliminary X-ray analysis of two hydrogen sulfide-producing enzymes from Fusobacterium nucleatum.,Kezuka Y, Abe N, Yoshida Y, Nonaka T Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Dec 1;68(Pt 12):1507-10., doi: 10.1107/S1744309112042546. Epub 2012 Nov 14. PMID:23192034<ref>PMID:23192034</ref>

-	~~Description: Crystal structure of~~ a ~~hydrogen sulfide~~-~~producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L~~-~~lanthionine-PLP Schiff base~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Nonaka, T~~]]	+	<div class="pdbe-citations 5xem" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cysteine synthase]]
	[[Category: Kezuka, Y]]		[[Category: Kezuka, Y]]
		+	[[Category: Nonaka, T]]
	[[Category: Yoshida, Y]]		[[Category: Yoshida, Y]]
		+	[[Category: Beta-replacement reaction]]
		+	[[Category: Hydrogen sulfide]]
		+	[[Category: L-cysteine]]
		+	[[Category: Lanthionine]]
		+	[[Category: Periodontal disease]]
		+	[[Category: Pyridoxal 5'-phosphate dependent enzyme]]
		+	[[Category: Transferase]]

OCA at 12:06, 4 May 2017

2017-05-04T12:06:54Z

←Older revision		Revision as of 12:06, 4 May 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xem is ON HOLD	+	The entry 5xem is ON HOLD until Paper Publication

	Authors: Kezuka, Y., Yoshida, Y., Nonaka, T.		Authors: Kezuka, Y., Yoshida, Y., Nonaka, T.

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

2017-04-12T10:41:51Z

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

←Older revision

Revision as of 10:41, 12 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xem is ON HOLD Authors: Kezuka, Y., Yoshida, Y., Nonaka, T. Description: Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fu...

2017-04-12T10:41:50Z

New page: '''Unreleased structure''' The entry 5xem is ON HOLD Authors: Kezuka, Y., Yoshida, Y., Nonaka, T. Description: Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fu...

New page

'''Unreleased structure'''

The entry 5xem is ON HOLD

Authors: Kezuka, Y., Yoshida, Y., Nonaka, T.

Description: Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-lanthionine-PLP Schiff base
[[Category: Unreleased Structures]]
[[Category: Nonaka, T]]
[[Category: Kezuka, Y]]
[[Category: Yoshida, Y]]