6vlo - Revision history

OCA at 08:14, 11 October 2023

2023-10-11T08:14:52Z

←Older revision		Revision as of 08:14, 11 October 2023
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	<StructureSection load='6vlo' size='340' side='right'caption='[[6vlo]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='6vlo' size='340' side='right'caption='[[6vlo]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vlo]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Apmv Apmv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VLO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VLO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vlo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VLO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VLO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NAD:NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE'>NAD</scene>~~, ~~<scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</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]] 2.05Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~MIMI_R141 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=212035 APMV])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/dTDP~~-~~glucose_4,6~~-~~dehydratase dTDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.46 4.2.1.46]~~ </~~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=6vlo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vlo OCA], [https://pdbe.org/6vlo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vlo RCSB], [https://www.ebi.ac.uk/pdbsum/6vlo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vlo 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=6vlo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vlo OCA], [~~http~~://pdbe.org/6vlo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vlo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vlo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vlo ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TGDS_MIMIV TGDS_MIMIV]
	<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: ~~Apmv~~]]	+	[[Category: Acanthamoeba polyphaga mimivirus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: DTDP-glucose 4,6-dehydratase]]~~	+	[[Category: Ferek JD]]
-	[[Category: Ferek~~, J D~~]]	+	[[Category: Holden HM]]
-	[[Category: Holden~~, H M~~]]	+	[[Category: Thoden JB]]
-	[[Category: Thoden~~, J B]]~~	+
-	~~[[Category: Acanthamoeba polyphaga minivirus]]~~	+
-	~~[[Category: Dehydratase]]~~	+
-	~~[[Category: Dideoxysugar]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Udp-viosamine~~]]	+

OCA at 06:00, 13 May 2020

2020-05-13T06:00:23Z

←Older revision		Revision as of 06:00, 13 May 2020
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	<StructureSection load='6vlo' size='340' side='right'caption='[[6vlo]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='6vlo' size='340' side='right'caption='[[6vlo]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vlo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VLO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6VLO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vlo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Apmv Apmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VLO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VLO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIMI_R141 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-glucose_4,6-dehydratase dTDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.46 4.2.1.46] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-glucose_4,6-dehydratase dTDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.46 4.2.1.46] </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=6vlo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vlo OCA], [http://pdbe.org/6vlo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vlo RCSB], [http://www.ebi.ac.uk/pdbsum/6vlo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vlo 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=6vlo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vlo OCA], [http://pdbe.org/6vlo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vlo RCSB], [http://www.ebi.ac.uk/pdbsum/6vlo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vlo ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Apmv]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: DTDP-glucose 4,6-dehydratase]]		[[Category: DTDP-glucose 4,6-dehydratase]]

OCA at 06:58, 4 March 2020

2020-03-04T06:58:13Z

←Older revision		Revision as of 06:58, 4 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6vlo is ~~ON HOLD until Paper~~ Publication	+	==X-ray Structure of the R141 Sugar 4,6-dehydratase from Acanthamoeba polyphaga Minivirus==
		+	<StructureSection load='6vlo' size='340' side='right'caption='[[6vlo]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6vlo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VLO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6VLO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-glucose_4,6-dehydratase dTDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.46 4.2.1.46] </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=6vlo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vlo OCA], [http://pdbe.org/6vlo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vlo RCSB], [http://www.ebi.ac.uk/pdbsum/6vlo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vlo ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The exciting discovery of the giant DNA Mimivirus in 2003 challenged the conventional description of viruses in a radical way, and since then, dozens of additional giant viruses have been identified. It has now been demonstrated that the Mimivirus genome encodes for the two enzymes required for the production of the unusual sugar 4-amino-4,6-dideoxy-d-glucose, namely a 4,6-dehydratase and an aminotransferase. In light of our long-standing interest in the bacterial 4,6-dehydratases and in unusual sugars in general, we conducted a combined structural and functional analysis of the Mimivirus 4,6-dehydratase referred to as R141. For this investigation, the three-dimensional X-ray structure of R141 was determined to 2.05 a resolution and refined to an R-factor of 18.3%. The overall fold of R141 places it into the short-chain dehydrogenase/reductase (SDR) superfamily of proteins. Whereas its molecular architecture is similar to that observed for the bacterial 4,6-dehydratases, there are two key regions where the polypeptide chain adopts different conformations. In particular, the conserved tyrosine that has been implicated as a catalytic acid or base in SDR superfamily members is splayed away from the active site by nearly 12 a, thereby suggesting that a major conformational change must occur upon substrate binding. In addition to the structural analysis, the kinetic parameters for R141 using either dTDP-d-glucose or UDP-d-glucose as substrates were determined. Contrary to a previous report, R141 demonstrates nearly identical catalytic efficiency with either nucleotide-linked sugar. The data presented herein represent the first three-dimensional model for a viral 4,6-dehydratase and thus expands our understanding of these fascinating enzymes. This article is protected by copyright. All rights reserved.

-	~~Authors: Thoden~~, ~~J.B~~., Ferek, ~~J.D.~~, Holden~~, H~~.M.	+	Biochemical Analysis of a Sugar 4,6-Dehydratase from Acanthamoeba polyphaga Mimivirus.,Ferek JD, Thoden JB, Holden HM Protein Sci. 2020 Feb 21. doi: 10.1002/pro.3843. PMID:32083779<ref>PMID:32083779</ref>

-	~~Description: X-ray Structure~~ of the ~~R141 Sugar 4,6~~-~~dehydratase from Acanthamoeba polyphaga Minivirus~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Thoden~~, ~~J.B~~]]	+	<div class="pdbe-citations 6vlo" style="background-color:#fffaf0;"></div>
-	[[Category: Ferek, J.D]]	+	== References ==
-	[[Category: Holden, H.M]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: DTDP-glucose 4,6-dehydratase]]
		+	[[Category: Ferek, J D]]
		+	[[Category: Holden, H M]]
		+	[[Category: Thoden, J B]]
		+	[[Category: Acanthamoeba polyphaga minivirus]]
		+	[[Category: Dehydratase]]
		+	[[Category: Dideoxysugar]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Udp-viosamine]]

OCA: Protected "6vlo" [edit=sysop:move=sysop]

2020-02-05T06:15:47Z

Protected "6vlo" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:15, 5 February 2020

OCA: New page: '''Unreleased structure''' The entry 6vlo is ON HOLD until Paper Publication Authors: Thoden, J.B., Ferek, J.D., Holden, H.M. Description: X-ray Structure of the R141 Sugar 4,6-dehydra...

2020-02-05T06:15:45Z

New page: '''Unreleased structure''' The entry 6vlo is ON HOLD until Paper Publication Authors: Thoden, J.B., Ferek, J.D., Holden, H.M. Description: X-ray Structure of the R141 Sugar 4,6-dehydra...

New page

'''Unreleased structure'''

The entry 6vlo is ON HOLD until Paper Publication

Authors: Thoden, J.B., Ferek, J.D., Holden, H.M.

Description: X-ray Structure of the R141 Sugar 4,6-dehydratase from Acanthamoeba polyphaga Minivirus
[[Category: Unreleased Structures]]
[[Category: Thoden, J.B]]
[[Category: Ferek, J.D]]
[[Category: Holden, H.M]]