7jid - Revision history

OCA at 15:03, 18 October 2023

OCA — Wed, 18 Oct 2023 15:03:31 GMT

←Older revision		Revision as of 15:03, 18 October 2023
Line 3:		Line 3:
	<StructureSection load='7jid' size='340' side='right'caption='[[7jid]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='7jid' size='340' side='right'caption='[[7jid]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7jid]] is a 2 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=7JID OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7JID FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jid]] is a 2 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=7JID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JID FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AWU:[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>AWU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 1.45Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIMI_L780 ([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=AWU:[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>AWU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></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=7jid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jid OCA], [~~http~~://pdbe.org/7jid PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7jid RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7jid PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7jid 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=7jid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jid OCA], [https://pdbe.org/7jid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jid RCSB], [https://www.ebi.ac.uk/pdbsum/7jid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jid ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/YL780_MIMIV YL780_MIMIV]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Apmv~~]]	+	[[Category: Acanthamoeba polyphaga mimivirus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bockhaus~~, N J~~]]	+	[[Category: Bockhaus NJ]]
-	[[Category: Ferek~~, J D~~]]	+	[[Category: Ferek JD]]
-	[[Category: Holden~~, H M~~]]	+	[[Category: Holden HM]]
-	[[Category: Thoden~~, J B]]~~	+	[[Category: Thoden JB]]
-	~~[[Category: Mimivirus]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rhamnose~~]]	+

OCA at 07:41, 4 November 2020

OCA — Wed, 04 Nov 2020 07:41:26 GMT

←Older revision		Revision as of 07:41, 4 November 2020
Line 1:		Line 1:

	==Crystal structure of the L780 UDP-rhamnose synthase from Acanthamoeba polyphaga mimivirus==		==Crystal structure of the L780 UDP-rhamnose synthase from Acanthamoeba polyphaga mimivirus==
-	<StructureSection load='7jid' size='340' side='right'caption='[[7jid]]' scene=''>	+	<StructureSection load='7jid' size='340' side='right'caption='[[7jid]], [[Resolution\|resolution]] 1.45Å' 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=7JID OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JID FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jid]] is a 2 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=7JID OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JID FirstGlance]. <br>
-	</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=7jid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jid OCA], [http://pdbe.org/7jid PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jid RCSB], [http://www.ebi.ac.uk/pdbsum/7jid PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jid 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=AWU:[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>AWU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIMI_L780 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</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=7jid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jid OCA], [http://pdbe.org/7jid PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jid RCSB], [http://www.ebi.ac.uk/pdbsum/7jid PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jid ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	For the field of virology, perhaps one of the most paradigm-shifting events so far in the 21(st) century was the identification of the giant double-stranded DNA virus that infects amoebae. Remarkably, this virus, known as Mimivirus, has a genome that encodes for nearly 1000 proteins, some of which are involved in the biosynthesis of unusual sugars. Indeed, the virus is coated by a layer of glycosylated fibers that contain d-glucose, N-acetyl-d-glucosamine, l-rhamnose, and 4-amino-4,6-dideoxy-d-glucose. Here we describe a combined structural and enzymological investigation of the protein encoded by the open-reading frame L780, which corresponds to an l-rhamnose synthase. The structure of the L780/NADP(+) /UDP-l-rhamnose ternary complex was determined to 1.45 A resolution and refined to an overall R-factor of 19.9 %. Each subunit of the dimeric protein adopts a bilobal-shaped appearance with the N-terminal domain harboring the dinucleotide binding site and the C-terminal domain positioning the UDP-sugar into the active site. The overall molecular architecture of L780 places it into the short chain dehydrogenase/reductase superfamily. Kinetic analyses indicate that the enzyme can function on either UDP- and dTDP-sugars but displays a higher catalytic efficiency with the UDP-linked substrate. Site-directed mutagenesis experiments suggest that both Cys 108 and Lys 175 play key roles in catalysis. This structure represents the first model of a viral UDP-l-rhamnose synthase and provides new details into these fascinating enzymes. This article is protected by copyright. All rights reserved.
		+
		+	The High-Resolution Structure of a UDP-l-Rhamnose Synthase from Acanthamoeba polyphaga Mimivirus.,Bockhaus NJ, Ferek JD, Thoden JB, Holden HM Protein Sci. 2020 Aug 14. doi: 10.1002/pro.3928. PMID:32797646<ref>PMID:32797646</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7jid" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Apmv]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bockhaus NJ]]	+	[[Category: Bockhaus, N J]]
-	[[Category: Ferek JD]]	+	[[Category: Ferek, J D]]
-	[[Category: Holden HM]]	+	[[Category: Holden, H M]]
-	[[Category: Thoden JB]]	+	[[Category: Thoden, J B]]
		+	[[Category: Mimivirus]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rhamnose]]

OCA at 11:20, 26 August 2020

OCA — Wed, 26 Aug 2020 11:20:03 GMT

←Older revision		Revision as of 11:20, 26 August 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7jid ~~is ON HOLD~~	+	==Crystal structure of the L780 UDP-rhamnose synthase from Acanthamoeba polyphaga mimivirus==
-		+	<StructureSection load='7jid' size='340' side='right'caption='[[7jid]]' scene=''>
-	~~Authors~~: ~~Bockhaus~~, N.J., ~~Ferek~~, J.D., ~~Thoden, J~~.B., ~~Holden, H~~.M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JID OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JID FirstGlance]. <br>
-	~~Description: Crystal structure of the L780 UDP-rhamnose synthase from Acanthamoeba polyphaga mimivirus~~	+	</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=7jid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jid OCA], [http://pdbe.org/7jid PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jid RCSB], [http://www.ebi.ac.uk/pdbsum/7jid PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jid ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Thoden, J.B~~]]	+	__TOC__
-	[[Category: ~~Holden, H.M~~]]	+	</StructureSection>
-	[[Category: ~~Ferek, J.D~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Bockhaus, N.J~~]]	+	[[Category: Bockhaus NJ]]
		+	[[Category: Ferek JD]]
		+	[[Category: Holden HM]]
		+	[[Category: Thoden JB]]

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

OCA — Wed, 29 Jul 2020 09:51:49 GMT

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

←Older revision

Revision as of 09:51, 29 July 2020

OCA: New page: '''Unreleased structure''' The entry 7jid is ON HOLD Authors: Bockhaus, N.J., Ferek, J.D., Thoden, J.B., Holden, H.M. Description: Crystal structure of the L780 UDP-rhamnose synthase f...

OCA — Wed, 29 Jul 2020 09:51:48 GMT

New page: '''Unreleased structure''' The entry 7jid is ON HOLD Authors: Bockhaus, N.J., Ferek, J.D., Thoden, J.B., Holden, H.M. Description: Crystal structure of the L780 UDP-rhamnose synthase f...

New page

'''Unreleased structure'''

The entry 7jid is ON HOLD

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

Description: Crystal structure of the L780 UDP-rhamnose synthase from Acanthamoeba polyphaga mimivirus
[[Category: Unreleased Structures]]
[[Category: Thoden, J.B]]
[[Category: Holden, H.M]]
[[Category: Ferek, J.D]]
[[Category: Bockhaus, N.J]]