6vvw - Revision history

OCA at 08:21, 11 October 2023

2023-10-11T08:21:50Z

←Older revision		Revision as of 08:21, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6vvw' size='340' side='right'caption='[[6vvw]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6vvw' size='340' side='right'caption='[[6vvw]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vvw]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Advenella_mimigardefordensis_dpn7~~ Advenella mimigardefordensis ~~dpn7~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VVW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VVW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vvw]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Advenella_mimigardefordensis_DPN7 Advenella mimigardefordensis DPN7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VVW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VVW FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~MIM_c08740 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1247726 Advenella mimigardefordensis DPN7])~~</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]] 2.1Å</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=6vvw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vvw OCA], [~~http~~://pdbe.org/6vvw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vvw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vvw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vvw 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=6vvw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vvw OCA], [https://pdbe.org/6vvw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vvw RCSB], [https://www.ebi.ac.uk/pdbsum/6vvw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vvw ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/W0PD56_ADVMD W0PD56_ADVMD]
	<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: Advenella mimigardefordensis ~~dpn7~~]]	+	[[Category: Advenella mimigardefordensis DPN7]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Medellin~~, B P~~]]	+	[[Category: Medellin BP]]
-	[[Category: Whitman~~, C P~~]]	+	[[Category: Whitman CP]]
-	[[Category: Zhang~~, Y J]]~~	+	[[Category: Zhang YJ]]
-	~~[[Category: 4-oxalocrotonate tautomerase]]~~	+
-	~~[[Category: Fused]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Symmetric~~]]	+

OCA at 06:01, 13 May 2020

2020-05-13T06:01:38Z

←Older revision		Revision as of 06:01, 13 May 2020
Line 1:		Line 1:

	==W0 fused 4-OT wild type symmetric trimer==		==W0 fused 4-OT wild type symmetric trimer==
-	<StructureSection load='6vvw' size='340' side='right'caption='[[6vvw]]' scene=''>	+	<StructureSection load='6vvw' size='340' side='right'caption='[[6vvw]], [[Resolution\|resolution]] 2.10Å' 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=6VVW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VVW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vvw]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Advenella_mimigardefordensis_dpn7 Advenella mimigardefordensis dpn7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VVW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VVW 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=6vvw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vvw OCA], [http://pdbe.org/6vvw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vvw RCSB], [http://www.ebi.ac.uk/pdbsum/6vvw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vvw ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIM_c08740 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1247726 Advenella mimigardefordensis DPN7])</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=6vvw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vvw OCA], [http://pdbe.org/6vvw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vvw RCSB], [http://www.ebi.ac.uk/pdbsum/6vvw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vvw ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tautomerase superfamily (TSF) members are constructed from a single beta-alpha-beta unit or two consecutively joined beta-alpha-beta units. This pattern prevails throughout the superfamily consisting of more than 11000 members where homo- or heterohexamers are localized in the 4-oxalocrotonate tautomerase (4-OT) subgroup and trimers are found in the other four subgroups. One exception is a subset of sequences that are double the length of the short 4-OTs in the 4-OT subgroup, where the coded proteins form trimers. Characterization of two members revealed an interesting dichotomy. One is a symmetric trimer, whereas the other is an asymmetric trimer. One monomer is flipped 180 degrees relative to the other two monomers so that three unique protein-protein interfaces are created that are composed of different residues. A bioinformatics analysis of the fused 4-OT subset shows a further division into two clusters with a total of 133 sequences. The analysis showed that members of one cluster (86 sequences) have more salt bridges if the asymmetric trimer forms, whereas the members of the other cluster (47 sequences) have more salt bridges if the symmetric trimer forms. This hypothesis was examined by the kinetic and structural characterization of two proteins within each cluster. As predicted, all four proteins function as 4-OTs, where two assemble into asymmetric trimers (designated R7 and F6) and two form symmetric trimers (designated W0 and Q0). These findings can be extended to the other sequences in the two clusters in the fused 4-OT subset, thereby annotating their oligomer properties and activities.
		+
		+	Structural Basis for the Asymmetry of a 4-Oxalocrotonate Tautomerase Trimer.,Medellin BP, Lancaster EB, Brown SD, Rakhade S, Babbitt PC, Whitman CP, Zhang YJ Biochemistry. 2020 Apr 13. doi: 10.1021/acs.biochem.0c00211. PMID:32242662<ref>PMID:32242662</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6vvw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Advenella mimigardefordensis dpn7]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Medellin BP]]	+	[[Category: Medellin, B P]]
-	[[Category: Whitman CP]]	+	[[Category: Whitman, C P]]
-	[[Category: Zhang YJ]]	+	[[Category: Zhang, Y J]]
		+	[[Category: 4-oxalocrotonate tautomerase]]
		+	[[Category: Fused]]
		+	[[Category: Isomerase]]
		+	[[Category: Symmetric]]

OCA at 07:03, 15 April 2020

2020-04-15T07:03:14Z

←Older revision		Revision as of 07:03, 15 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6vvw ~~is ON HOLD until Paper Publication~~	+	==W0 fused 4-OT wild type symmetric trimer==
-		+	<StructureSection load='6vvw' size='340' side='right'caption='[[6vvw]]' scene=''>
-	~~Authors~~: ~~Medellin~~, B.P., ~~Whitman~~, C.P., ~~Zhang~~, Y.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VVW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VVW FirstGlance]. <br>
-	~~Description: W0 fused 4-OT wild type symmetric trimer~~	+	</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=6vvw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vvw OCA], [http://pdbe.org/6vvw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vvw RCSB], [http://www.ebi.ac.uk/pdbsum/6vvw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vvw ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Whitman, C.P~~]]	+	__TOC__
-	[[Category: ~~Zhang, Y.J~~]]	+	</StructureSection>
-	[[Category: ~~Medellin, B.P~~]]	+	[[Category: Large Structures]]
		+	[[Category: Medellin BP]]
		+	[[Category: Whitman CP]]
		+	[[Category: Zhang YJ]]

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

2020-02-26T08:12:57Z

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

←Older revision

Revision as of 08:12, 26 February 2020

OCA: New page: '''Unreleased structure''' The entry 6vvw is ON HOLD until Paper Publication Authors: Medellin, B.P., Whitman, C.P., Zhang, Y.J. Description: W0 fused 4-OT wild type symmetric trimer [...

2020-02-26T08:12:56Z

New page: '''Unreleased structure''' The entry 6vvw is ON HOLD until Paper Publication Authors: Medellin, B.P., Whitman, C.P., Zhang, Y.J. Description: W0 fused 4-OT wild type symmetric trimer [...

New page

'''Unreleased structure'''

The entry 6vvw is ON HOLD until Paper Publication

Authors: Medellin, B.P., Whitman, C.P., Zhang, Y.J.

Description: W0 fused 4-OT wild type symmetric trimer
[[Category: Unreleased Structures]]
[[Category: Whitman, C.P]]
[[Category: Zhang, Y.J]]
[[Category: Medellin, B.P]]