5xny - Revision history

OCA at 08:07, 22 November 2023

OCA — Wed, 22 Nov 2023 08:07:22 GMT

←Older revision		Revision as of 08:07, 22 November 2023
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	==Crystal structure of CreD==		==Crystal structure of CreD==
-	<StructureSection load='5xny' size='340' side='right' caption='[[5xny]], [[Resolution\|resolution]] 2.18Å' scene=''>	+	<StructureSection load='5xny' size='340' side='right'caption='[[5xny]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xny]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"actinomyces_cremeus"_kudrina_in_gauze_et_al._1957 "actinomyces~~ cremeus~~" kudrina in gauze et al. 1957~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xny]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_cremeus Streptomyces cremeus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XNY FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>creD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~66881~~ "~~Actinomyces cremeus~~" ~~Kudrina in Gauze et al~~. ~~1957])~~</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]] 2.18Å</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=5xny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xny OCA], [~~http~~://pdbe.org/5xny PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xny RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xny PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xny 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=5xny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xny OCA], [https://pdbe.org/5xny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xny RCSB], [https://www.ebi.ac.uk/pdbsum/5xny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xny ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0K2JL82_9ACTN A0A0K2JL82_9ACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Actinomyces~~ cremeus ~~kudrina in gauze et al. 1957~~]]	+	[[Category: Large Structures]]
-	[[Category: Higashiyama, Y]]	+	[[Category: Streptomyces cremeus]]
-	[[Category: Katsuyama, Y]]	+	[[Category: Higashiyama Y]]
-	[[Category: Ohnishi, Y]]	+	[[Category: Katsuyama Y]]
-	[[Category: Sato, Y]]	+	[[Category: Ohnishi Y]]
-	[[Category: Senda, M]]	+	[[Category: Sato Y]]
-	[[Category: Senda, T]]	+	[[Category: Senda M]]
-	[[Category: Sugai, Y]]	+	[[Category: Senda T]]
-	~~[[Category: Aspartase]]~~	+	[[Category: Sugai Y]]
-	~~[[Category: Cremeomycin]]~~	+
-	~~[[Category: Fumarase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Nitrous acid~~]]	+

OCA at 07:59, 21 March 2018

OCA — Wed, 21 Mar 2018 07:59:43 GMT

←Older revision		Revision as of 07:59, 21 March 2018
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	<StructureSection load='5xny' size='340' side='right' caption='[[5xny]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='5xny' size='340' side='right' caption='[[5xny]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xny]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xny]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_cremeus"_kudrina_in_gauze_et_al._1957 "actinomyces cremeus" kudrina in gauze et al. 1957]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XNY FirstGlance]. <br>
-	</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=5xny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xny OCA], [http://pdbe.org/5xny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xny RCSB], [http://www.ebi.ac.uk/pdbsum/5xny PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xny ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">creD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=66881 "Actinomyces cremeus" Kudrina in Gauze et al. 1957])</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=5xny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xny OCA], [http://pdbe.org/5xny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xny RCSB], [http://www.ebi.ac.uk/pdbsum/5xny PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xny ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Enzymes belonging to the aspartase/fumarase superfamily catalyze elimination of various functional groups from succinate derivatives and play an important role in primary metabolism and aromatic compound degradation. Recently, an aspartase/fumarase superfamily enzyme, CreD, was discovered in cremeomycin biosynthesis. This enzyme catalyzes the elimination of nitrous acid from nitrosuccinate synthesized from aspartate by CreE, a flavin-dependent monooxygenase. Nitrous acid generated by this pathway is an important precursor of the diazo group of cremeomycin. CreD is the first aspartase/fumarase superfamily enzyme that was reported to catalyze the elimination of nitrous acid, and therefore we aimed to analyze its reaction mechanism. The crystal structure of CreD was determined by the molecular replacement native-single anomalous diffraction (MR native-SAD) method at 2.18 A resolution. Subsequently, the CreD-fumarate complex structure was determined at 2.30 A resolution by the soaking method. Similar to other aspartase/fumarase superfamily enzymes, the crystal structure of CreD was composed of three domains and formed a tetramer. Two molecules of fumarate were observed in one subunit of the CreD-fumarate complex. One of them was located in the active site pocket formed by three different subunits. Intriguingly, no histidine residue, which usually functions as a catalytic acid in aspartase/fumarase superfamily enzymes, was found around the fumarate molecule in the active site. Based on the mutational analysis, we propose a catalytic mechanism of CreD, in which Arg325 acts as a catalytic acid. This article is protected by copyright. All rights reserved.
		+
		+	Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination.,Katsuyama Y, Sato Y, Sugai Y, Higashiyama Y, Senda M, Senda T, Ohnishi Y FEBS J. 2018 Mar 5. doi: 10.1111/febs.14429. PMID:29505698<ref>PMID:29505698</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xny" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Actinomyces cremeus kudrina in gauze et al. 1957]]
	[[Category: Higashiyama, Y]]		[[Category: Higashiyama, Y]]
	[[Category: Katsuyama, Y]]		[[Category: Katsuyama, Y]]

OCA at 06:26, 14 March 2018

OCA — Wed, 14 Mar 2018 06:26:14 GMT

←Older revision		Revision as of 06:26, 14 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xny is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of CreD==
-		+	<StructureSection load='5xny' size='340' side='right' caption='[[5xny]], [[Resolution\|resolution]] 2.18Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xny]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XNY FirstGlance]. <br>
-	~~Description~~:	+	</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=5xny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xny OCA], [http://pdbe.org/5xny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xny RCSB], [http://www.ebi.ac.uk/pdbsum/5xny PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xny ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Higashiyama, Y]]
		+	[[Category: Katsuyama, Y]]
		+	[[Category: Ohnishi, Y]]
		+	[[Category: Sato, Y]]
		+	[[Category: Senda, M]]
		+	[[Category: Senda, T]]
		+	[[Category: Sugai, Y]]
		+	[[Category: Aspartase]]
		+	[[Category: Cremeomycin]]
		+	[[Category: Fumarase]]
		+	[[Category: Lyase]]
		+	[[Category: Nitrous acid]]

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

OCA — Wed, 27 Sep 2017 15:36:52 GMT

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

←Older revision

Revision as of 15:36, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xny is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 15:36:50 GMT

New page: '''Unreleased structure''' The entry 5xny is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xny is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]