1yov - Revision history

OCA at 08:58, 14 February 2024

OCA — Wed, 14 Feb 2024 08:58:39 GMT

←Older revision		Revision as of 08:58, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1yov' size='340' side='right'caption='[[1yov]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='1yov' size='340' side='right'caption='[[1yov]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yov]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1YOV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yov]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YOV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1r4n\|1r4n]]~~, [[~~1r4m~~\|~~1r4m]], [[1tt5\|1tt5]], [[1y8x\|1y8x~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~APPBP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN]), UBE1C, UBA3 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=1yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yov OCA], [https://pdbe.org/1yov PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yov RCSB], [https://www.ebi.ac.uk/pdbsum/1yov PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yov 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=1yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yov OCA], [~~http~~://pdbe.org/1yov PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1yov RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1yov PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1yov ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/ULA1_HUMAN ULA1_HUMAN]] Regulatory subunit of the dimeric UBA3-NAE1 E1 enzyme. E1 activates NEDD8 by first adenylating its C-terminal glycine residue with ATP, thereafter linking this residue to the side chain of the catalytic cysteine, yielding a NEDD8-UBA3 thioester and free AMP. E1 finally transfers NEDD8 to the catalytic cysteine of UBE2M. Necessary for cell cycle progression through the S-M checkpoint. Overexpression of NAE1 causes apoptosis through deregulation of NEDD8 conjugation.<ref>PMID:10207026</ref> <ref>PMID:10722740</ref> <ref>PMID:12740388</ref> [[http://www.uniprot.org/uniprot/UBA3_HUMAN UBA3_HUMAN]] Catalytic subunit of the dimeric UBA3-NAE1 E1 enzyme. E1 activates NEDD8 by first adenylating its C-terminal glycine residue with ATP, thereafter linking this residue to the side chain of the catalytic cysteine, yielding a NEDD8-UBA3 thioester and free AMP. E1 finally transfers NEDD8 to the catalytic cysteine of UBE2M. Down-regulates steroid receptor activity. Necessary for cell cycle progression.<ref>PMID:10207026</ref> <ref>PMID:9694792</ref> <ref>PMID:12740388</ref>	+	[https://www.uniprot.org/uniprot/UBA3_HUMAN UBA3_HUMAN] Catalytic subunit of the dimeric UBA3-NAE1 E1 enzyme. E1 activates NEDD8 by first adenylating its C-terminal glycine residue with ATP, thereafter linking this residue to the side chain of the catalytic cysteine, yielding a NEDD8-UBA3 thioester and free AMP. E1 finally transfers NEDD8 to the catalytic cysteine of UBE2M. Down-regulates steroid receptor activity. Necessary for cell cycle progression.<ref>PMID:10207026</ref> <ref>PMID:9694792</ref> <ref>PMID:12740388</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1yov ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1yov ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Post-translational modification by ubiquitin-like proteins (Ublps) is an essential cellular regulatory mechanism. The Ublp NEDD8 regulates cell division, signalling and embryogenesis. Ublps are conjugated to their targets by the sequential action of E1, E2 and often E3 enzymes. Each Ublp has a dedicated E1, or activating enzyme, that initiates its conjugation cascade. First, E1 associates with the Ublp and catalyses adenylation of the carboxy terminus of the Ublp. Second, E1 forms a thioester between its catalytic cysteine and the Ublp. Next, E1 is loaded with a second Ublp molecule, adenylating the C terminus of this second Ublp while still carrying the first thioester-bound Ublp. Last, E1 binds E2 and promotes Ublp transfer to the catalytic cysteine of E2. We report here the structure and mutational analysis of human APPBP1-UBA3, the heterodimeric E1 enzyme for NEDD8 (ref. 11). Each E1 activity is specified by a domain: an adenylation domain resembling bacterial adenylating enzymes, an E1-specific domain organized around the catalytic cysteine, and a domain involved in E2 recognition resembling ubiquitin. The domains are arranged around two clefts that coordinate protein and nucleotide binding so that each of E1's reactions drives the next, in an assembly-line fashion.
-
-	Insights into the ubiquitin transfer cascade from the structure of the activating enzyme for NEDD8.,Walden H, Podgorski MS, Schulman BA Nature. 2003 Mar 20;422(6929):330-4. PMID:12646924<ref>PMID:12646924</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1yov" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Ubiquitin activating enzyme\|Ubiquitin activating enzyme]]	+	*[[3D structures of Ubiquitin activating enzyme\|3D structures of Ubiquitin activating enzyme]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Podgorski~~, M S~~]]	+	[[Category: Podgorski MS]]
-	[[Category: Schulman~~, B A~~]]	+	[[Category: Schulman BA]]
-	[[Category: Walden, H]]	+	[[Category: Walden H]]
-	~~[[Category: Appbp1]]~~	+
-	~~[[Category: E1]]~~	+
-	~~[[Category: Nedd8]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Uba3]]~~	+
-	~~[[Category: Ubiquitin~~]]	+

OCA at 08:49, 20 January 2021

OCA — Wed, 20 Jan 2021 08:49:50 GMT

←Older revision		Revision as of 08:49, 20 January 2021
Line 1:		Line 1:

	==Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8==		==Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8==
-	<StructureSection load='1yov' size='340' side='right' caption='[[1yov]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='1yov' size='340' side='right'caption='[[1yov]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yov]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YOV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yov]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YOV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r4n\|1r4n]], [[1r4m\|1r4m]], [[1tt5\|1tt5]], [[1y8x\|1y8x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1r4n\|1r4n]], [[1r4m\|1r4m]], [[1tt5\|1tt5]], [[1y8x\|1y8x]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APPBP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UBE1C, UBA3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APPBP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UBE1C, UBA3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yov OCA], [http://pdbe.org/1yov PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yov RCSB], [http://www.ebi.ac.uk/pdbsum/1yov PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yov 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=1yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yov OCA], [http://pdbe.org/1yov PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yov RCSB], [http://www.ebi.ac.uk/pdbsum/1yov PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yov ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Podgorski, M S]]		[[Category: Podgorski, M S]]
	[[Category: Schulman, B A]]		[[Category: Schulman, B A]]

OCA at 06:42, 25 April 2018

OCA — Wed, 25 Apr 2018 06:42:24 GMT

←Older revision		Revision as of 06:42, 25 April 2018
Line 1:		Line 1:
		+
	==Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8==		==Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8==
	<StructureSection load='1yov' size='340' side='right' caption='[[1yov]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='1yov' size='340' side='right' caption='[[1yov]], [[Resolution\|resolution]] 2.60Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r4n\|1r4n]], [[1r4m\|1r4m]], [[1tt5\|1tt5]], [[1y8x\|1y8x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r4n\|1r4n]], [[1r4m\|1r4m]], [[1tt5\|1tt5]], [[1y8x\|1y8x]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APPBP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UBE1C, UBA3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APPBP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UBE1C, UBA3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yov OCA], [http://pdbe.org/1yov PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yov RCSB], [http://www.ebi.ac.uk/pdbsum/1yov 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=1yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yov OCA], [http://pdbe.org/1yov PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yov RCSB], [http://www.ebi.ac.uk/pdbsum/1yov PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yov ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yo/1yov_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yo/1yov_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 18:40, 7 February 2016

OCA — Sun, 07 Feb 2016 18:40:00 GMT

←Older revision		Revision as of 18:40, 7 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1yov ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:08, 10 September 2015

OCA — Thu, 10 Sep 2015 04:08:02 GMT

←Older revision		Revision as of 04:08, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1yov' size='340' side='right' caption='[[1yov]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='1yov' size='340' side='right' caption='[[1yov]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yov]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YOV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yov]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YOV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r4n\|1r4n]], [[1r4m\|1r4m]], [[1tt5\|1tt5]], [[1y8x\|1y8x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r4n\|1r4n]], [[1r4m\|1r4m]], [[1tt5\|1tt5]], [[1y8x\|1y8x]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APPBP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~]), UBE1C, UBA3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APPBP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UBE1C, UBA3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yov OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yov RCSB], [http://www.ebi.ac.uk/pdbsum/1yov 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=1yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yov OCA], [http://pdbe.org/1yov PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yov RCSB], [http://www.ebi.ac.uk/pdbsum/1yov PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1yov" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Podgorski, M S]]		[[Category: Podgorski, M S]]
	[[Category: Schulman, B A]]		[[Category: Schulman, B A]]

OCA at 17:30, 24 December 2014

OCA — Wed, 24 Dec 2014 17:30:36 GMT

←Older revision		Revision as of 17:30, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yov]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YOV FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yov]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YOV FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r4n\|1r4n]], [[1r4m\|1r4m]], [[1tt5\|1tt5]], [[1y8x\|1y8x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r4n\|1r4n]], [[1r4m\|1r4m]], [[1tt5\|1tt5]], [[1y8x\|1y8x]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APPBP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), UBE1C, UBA3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APPBP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), UBE1C, UBA3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yov OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yov RCSB], [http://www.ebi.ac.uk/pdbsum/1yov 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=1yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yov OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yov RCSB], [http://www.ebi.ac.uk/pdbsum/1yov PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ULA1_HUMAN ULA1_HUMAN]] Regulatory subunit of the dimeric UBA3-NAE1 E1 enzyme. E1 activates NEDD8 by first adenylating its C-terminal glycine residue with ATP, thereafter linking this residue to the side chain of the catalytic cysteine, yielding a NEDD8-UBA3 thioester and free AMP. E1 finally transfers NEDD8 to the catalytic cysteine of UBE2M. Necessary for cell cycle progression through the S-M checkpoint. Overexpression of NAE1 causes apoptosis through deregulation of NEDD8 conjugation.<ref>PMID:10207026</ref> <ref>PMID:10722740</ref> <ref>PMID:12740388</ref> [[http://www.uniprot.org/uniprot/UBA3_HUMAN UBA3_HUMAN]] Catalytic subunit of the dimeric UBA3-NAE1 E1 enzyme. E1 activates NEDD8 by first adenylating its C-terminal glycine residue with ATP, thereafter linking this residue to the side chain of the catalytic cysteine, yielding a NEDD8-UBA3 thioester and free AMP. E1 finally transfers NEDD8 to the catalytic cysteine of UBE2M. Down-regulates steroid receptor activity. Necessary for cell cycle progression.<ref>PMID:10207026</ref> <ref>PMID:9694792</ref> <ref>PMID:12740388</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Podgorski, M S.]]	+	[[Category: Podgorski, M S]]
-	[[Category: Schulman, B A.]]	+	[[Category: Schulman, B A]]
-	[[Category: Walden, H.]]	+	[[Category: Walden, H]]
	[[Category: Appbp1]]		[[Category: Appbp1]]
	[[Category: E1]]		[[Category: E1]]

OCA at 18:32, 29 September 2014

OCA — Mon, 29 Sep 2014 18:32:49 GMT

←Older revision		Revision as of 18:32, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1yov.~~png~~\|~~left~~\|200px]]	+	==Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8==
		+	<StructureSection load='1yov' size='340' side='right' caption='[[1yov]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1yov]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YOV FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r4n\|1r4n]], [[1r4m\|1r4m]], [[1tt5\|1tt5]], [[1y8x\|1y8x]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APPBP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), UBE1C, UBA3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yov OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yov RCSB], [http://www.ebi.ac.uk/pdbsum/1yov PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yo/1yov_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Post-translational modification by ubiquitin-like proteins (Ublps) is an essential cellular regulatory mechanism. The Ublp NEDD8 regulates cell division, signalling and embryogenesis. Ublps are conjugated to their targets by the sequential action of E1, E2 and often E3 enzymes. Each Ublp has a dedicated E1, or activating enzyme, that initiates its conjugation cascade. First, E1 associates with the Ublp and catalyses adenylation of the carboxy terminus of the Ublp. Second, E1 forms a thioester between its catalytic cysteine and the Ublp. Next, E1 is loaded with a second Ublp molecule, adenylating the C terminus of this second Ublp while still carrying the first thioester-bound Ublp. Last, E1 binds E2 and promotes Ublp transfer to the catalytic cysteine of E2. We report here the structure and mutational analysis of human APPBP1-UBA3, the heterodimeric E1 enzyme for NEDD8 (ref. 11). Each E1 activity is specified by a domain: an adenylation domain resembling bacterial adenylating enzymes, an E1-specific domain organized around the catalytic cysteine, and a domain involved in E2 recognition resembling ubiquitin. The domains are arranged around two clefts that coordinate protein and nucleotide binding so that each of E1's reactions drives the next, in an assembly-line fashion.

-	~~{{STRUCTURE_1yov\| PDB=1yov \| SCENE= }}~~	+	Insights into the ubiquitin transfer cascade from the structure of the activating enzyme for NEDD8.,Walden H, Podgorski MS, Schulman BA Nature. 2003 Mar 20;422(6929):330-4. PMID:12646924<ref>PMID:12646924</ref>

-	~~===Insights into~~ the ~~Ubiquitin Transfer Cascade from the refined structure~~ of ~~the activating enzyme for NEDD8===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_12646924}}~~	+	==See Also==
-		+	*[[Ubiquitin activating enzyme\|Ubiquitin activating enzyme]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1yov~~]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:012646924<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Podgorski, M S.]]		[[Category: Podgorski, M S.]]

OCA: Protected "1yov" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 17:20:28 GMT

Protected "1yov" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:20, 5 January 2013

OCA at 17:20, 5 January 2013

OCA — Sat, 05 Jan 2013 17:20:25 GMT

←Older revision		Revision as of 17:20, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1yov.png\|left\|200px]]		[[Image:1yov.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1yov", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1yov\| PDB=1yov \| SCENE= }}		{{STRUCTURE_1yov\| PDB=1yov \| SCENE= }}

	===Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8===		===Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12646924}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12646924 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12646924}}		{{ABSTRACT_PUBMED_12646924}}

	==About this Structure==		==About this Structure==
-	~~1YOV~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA].	+	[[1yov]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12646924~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012646924</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Podgorski, M S.]]		[[Category: Podgorski, M S.]]
Line 31:		Line 19:
	[[Category: E1]]		[[Category: E1]]
	[[Category: Nedd8]]		[[Category: Nedd8]]
		+	[[Category: Signaling protein]]
	[[Category: Uba3]]		[[Category: Uba3]]
	[[Category: Ubiquitin]]		[[Category: Ubiquitin]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:49:23 2009''

OCA at 13:49, 16 February 2009

OCA — Mon, 16 Feb 2009 13:49:24 GMT

←Older revision		Revision as of 13:49, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1YOV is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA].	+	1YOV is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ngv 1ngv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YOV OCA].

	==Reference==		==Reference==
-	~~Insights into the ubiquitin transfer cascade from the structure of the activating enzyme for NEDD8., Walden H, Podgorski MS, Schulman BA, Nature. 2003 Mar 20;422(6929):330-4.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12646924 12646924]~~	+	<ref group="xtra">PMID:12646924</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Protein complex]]
	[[Category: Podgorski, M S.]]		[[Category: Podgorski, M S.]]
	[[Category: Schulman, B A.]]		[[Category: Schulman, B A.]]
Line 35:		Line 34:
	[[Category: Ubiquitin]]		[[Category: Ubiquitin]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 18~~:49:~~34 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:49:23 2009''