4od4 - Revision history

OCA at 12:39, 1 March 2024

2024-03-01T12:39:12Z

←Older revision		Revision as of 12:39, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4od4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OD4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4od4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OD4 FirstGlance]. <br>
-	</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=4od4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4od4 OCA], [https://pdbe.org/4od4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4od4 RCSB], [https://www.ebi.ac.uk/pdbsum/4od4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4od4 ProSAT]</span></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]] 3.301Å</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=4od4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4od4 OCA], [https://pdbe.org/4od4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4od4 RCSB], [https://www.ebi.ac.uk/pdbsum/4od4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4od4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q9YBM8_AERPE Q9YBM8_AERPE]		[https://www.uniprot.org/uniprot/Q9YBM8_AERPE Q9YBM8_AERPE]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Biosynthesis of ubiquinones requires the intramembrane UbiA enzyme, an archetypal member of a superfamily of prenyltransferases that generates lipophilic aromatic compounds. Mutations in eukaryotic superfamily members have been linked to cardiovascular degeneration and Parkinson's disease. To understand how quinones are produced within membranes, we report the crystal structures of an archaeal UbiA in its apo and substrate-bound states at 3.3 and 3.6 angstrom resolution, respectively. The structures reveal nine transmembrane helices and an extramembrane cap domain that surround a large central cavity containing the active site. To facilitate the catalysis inside membranes, UbiA has an unusual active site that opens laterally to the lipid bilayer. Our studies illuminate general mechanisms for substrate recognition and catalysis in the UbiA superfamily and rationalize disease-related mutations in humans.
-
-	Structural insights into ubiquinone biosynthesis in membranes.,Cheng W, Li W Science. 2014 Feb 21;343(6173):878-81. doi: 10.1126/science.1246774. PMID:24558159<ref>PMID:24558159</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4od4" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:17, 25 January 2023

2023-01-25T07:17:56Z

←Older revision		Revision as of 07:17, 25 January 2023
Line 1:		Line 1:

	==Apo structure of a UbiA homolog from Aeropyrum pernix K1==		==Apo structure of a UbiA homolog from Aeropyrum pernix K1==
-	<StructureSection load='4od4' size='340' side='right' caption='[[4od4]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<StructureSection load='4od4' size='340' side='right'caption='[[4od4]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4od4]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aerpe Aerpe~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OD4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4OD4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4od4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OD4 FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4od5\|4od5]]</td></tr>~~	+	</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=4od4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4od4 OCA], [https://pdbe.org/4od4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4od4 RCSB], [https://www.ebi.ac.uk/pdbsum/4od4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4od4 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ubiA, APE_1570 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</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=4od4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4od4 OCA], [~~http~~://pdbe.org/4od4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4od4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4od4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4od4 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9YBM8_AERPE Q9YBM8_AERPE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aerpe~~]]	+	[[Category: Aeropyrum pernix K1]]
-	[[Category: ~~Cheng, W~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Li,~~ W]]	+	[[Category: Cheng W]]
-	[[Category: ~~All alpha helical]]~~	+	[[Category: Li W]]
-	~~[[Category: Intramembrane aromatic prenyltransferase]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 17:12, 11 August 2016

2016-08-11T17:12:23Z

←Older revision		Revision as of 17:12, 11 August 2016
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		+
	==Apo structure of a UbiA homolog from Aeropyrum pernix K1==		==Apo structure of a UbiA homolog from Aeropyrum pernix K1==
	<StructureSection load='4od4' size='340' side='right' caption='[[4od4]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='4od4' size='340' side='right' caption='[[4od4]], [[Resolution\|resolution]] 3.30Å' scene=''>
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	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4od5\|4od5]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4od5\|4od5]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ubiA, APE_1570 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ubiA, APE_1570 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</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=4od4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4od4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4od4 RCSB], [http://www.ebi.ac.uk/pdbsum/4od4 PDBsum]</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=4od4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4od4 OCA], [http://pdbe.org/4od4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4od4 RCSB], [http://www.ebi.ac.uk/pdbsum/4od4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4od4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4od4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:32, 5 January 2015

2015-01-05T09:32:41Z

←Older revision		Revision as of 09:32, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4od4\| PDB=4od4 \| SCENE= }}~~	+	==Apo structure of a UbiA homolog from Aeropyrum pernix K1==
-	===Apo structure of a UbiA homolog from Aeropyrum pernix K1===	+	<StructureSection load='4od4' size='340' side='right' caption='[[4od4]], [[Resolution\|resolution]] 3.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24558159}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4od4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OD4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OD4 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4od5\|4od5]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ubiA, APE_1570 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</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=4od4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4od4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4od4 RCSB], [http://www.ebi.ac.uk/pdbsum/4od4 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Biosynthesis of ubiquinones requires the intramembrane UbiA enzyme, an archetypal member of a superfamily of prenyltransferases that generates lipophilic aromatic compounds. Mutations in eukaryotic superfamily members have been linked to cardiovascular degeneration and Parkinson's disease. To understand how quinones are produced within membranes, we report the crystal structures of an archaeal UbiA in its apo and substrate-bound states at 3.3 and 3.6 angstrom resolution, respectively. The structures reveal nine transmembrane helices and an extramembrane cap domain that surround a large central cavity containing the active site. To facilitate the catalysis inside membranes, UbiA has an unusual active site that opens laterally to the lipid bilayer. Our studies illuminate general mechanisms for substrate recognition and catalysis in the UbiA superfamily and rationalize disease-related mutations in humans.

-	~~==About this Structure==~~	+	Structural insights into ubiquinone biosynthesis in membranes.,Cheng W, Li W Science. 2014 Feb 21;343(6173):878-81. doi: 10.1126/science.1246774. PMID:24558159<ref>PMID:24558159</ref>
-	~~[[4od4]] is a 6 chain structure~~. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4OD4 OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024558159</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Cheng, W.]]	+	== References ==
-	[[Category: Li, W.]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Aerpe]]
		+	[[Category: Cheng, W]]
		+	[[Category: Li, W]]
	[[Category: All alpha helical]]		[[Category: All alpha helical]]
	[[Category: Intramembrane aromatic prenyltransferase]]		[[Category: Intramembrane aromatic prenyltransferase]]
	[[Category: Membrane]]		[[Category: Membrane]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 08:41, 19 March 2014

2014-03-19T08:41:37Z

←Older revision		Revision as of 08:41, 19 March 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4od4\| PDB=4od4 \| SCENE= }}
		+	===Apo structure of a UbiA homolog from Aeropyrum pernix K1===
		+	{{ABSTRACT_PUBMED_24558159}}

-	~~The entry~~ 4od4 is ~~ON HOLD~~	+	==About this Structure==
		+	[[4od4]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OD4 OCA].

-	~~Authors~~: Li, W.~~, Cheng~~, W.	+	==Reference==
-		+	<ref group="xtra">PMID:024558159</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Apo structure of a UbiA homolog from Aeropyrum pernix K1~~	+	[[Category: Cheng, W.]]
		+	[[Category: Li, W.]]
		+	[[Category: All alpha helical]]
		+	[[Category: Intramembrane aromatic prenyltransferase]]
		+	[[Category: Membrane]]
		+	[[Category: Transferase]]

OCA: Protected "4od4" [edit=sysop:move=sysop]

2014-01-15T07:47:17Z

Protected "4od4" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:47, 15 January 2014

OCA: New page: '''Unreleased structure''' The entry 4od4 is ON HOLD Authors: Li, W., Cheng, W. Description: Apo structure of a UbiA homolog from Aeropyrum pernix K1

2014-01-15T07:47:16Z

New page: '''Unreleased structure''' The entry 4od4 is ON HOLD Authors: Li, W., Cheng, W. Description: Apo structure of a UbiA homolog from Aeropyrum pernix K1

New page

'''Unreleased structure'''

The entry 4od4 is ON HOLD

Authors: Li, W., Cheng, W.

Description: Apo structure of a UbiA homolog from Aeropyrum pernix K1