2grr - Revision history

OCA at 09:29, 14 February 2024

2024-02-14T09:29:36Z

←Older revision		Revision as of 09:29, 14 February 2024
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	<StructureSection load='2grr' size='340' side='right'caption='[[2grr]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='2grr' size='340' side='right'caption='[[2grr]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2grr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GRR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2grr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GRR FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2grn\|2grn]], [[2gro\|2gro]], [[2grp\|2grp]], [[2grq\|2grq]]</div></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]] 1.3Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">UBE2I, UBC9, UBCE9 ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=9606 HUMAN]), RANGAP1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </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=2grr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2grr OCA], [https://pdbe.org/2grr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2grr RCSB], [https://www.ebi.ac.uk/pdbsum/2grr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2grr 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=2grr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2grr OCA], [https://pdbe.org/2grr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2grr RCSB], [https://www.ebi.ac.uk/pdbsum/2grr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2grr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/UBC9_HUMAN UBC9_HUMAN]] Accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3 and SUMO4 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2 or CBX4. Can catalyze the formation of poly-SUMO chains. Necessary for sumoylation of FOXL2 and KAT5. Essential for nuclear architecture and chromosome segregation.<ref>PMID:8668529</ref> <ref>PMID:11451954</ref> <ref>PMID:15809060</ref> <ref>PMID:19744555</ref> <ref>PMID:19638400</ref> <ref>PMID:17466333</ref> <ref>PMID:20077568</ref>	+	[https://www.uniprot.org/uniprot/UBC9_HUMAN UBC9_HUMAN] Accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3 and SUMO4 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2 or CBX4. Can catalyze the formation of poly-SUMO chains. Necessary for sumoylation of FOXL2 and KAT5. Essential for nuclear architecture and chromosome segregation.<ref>PMID:8668529</ref> <ref>PMID:11451954</ref> <ref>PMID:15809060</ref> <ref>PMID:19744555</ref> <ref>PMID:19638400</ref> <ref>PMID:17466333</ref> <ref>PMID:20077568</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=2grr 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=2grr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	E2 conjugating proteins that transfer ubiquitin and ubiquitin-like modifiers to substrate lysine residues must first activate the lysine nucleophile for conjugation. Genetic complementation revealed three side chains of the E2 Ubc9 that were crucial for normal growth. Kinetic analysis revealed modest binding defects but substantially lowered catalytic rates for these mutant alleles with respect to wild-type Ubc9. X-ray structures for wild-type and mutant human Ubc9-RanGAP1 complexes showed partial loss of contacts to the substrate lysine in mutant complexes. Computational analysis predicted pK perturbations for the substrate lysine, and Ubc9 mutations weakened pK suppression through improper side chain coordination. Biochemical studies with p53, RanGAP1 and the Nup358/RanBP2 E3 were used to determine rate constants and pK values, confirming both structural and computational predictions. It seems that Ubc9 uses an indirect mechanism to activate lysine for conjugation that may be conserved among E2 family members.
-
-	Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway.,Yunus AA, Lima CD Nat Struct Mol Biol. 2006 Jun;13(6):491-9. Epub 2006 May 28. PMID:16732283<ref>PMID:16732283</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2grr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ubiquitin--protein ligase]]~~	+	[[Category: Lima CD]]
-	[[Category: Lima~~, C D~~]]	+	[[Category: Yunus AA]]
-	[[Category: Yunus~~, A A]]~~	+
-	~~[[Category: Conjugation]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Small ubiquitin like modifer]]~~	+
-	~~[[Category: Smt3]]~~	+
-	~~[[Category: Ubiquitin~~]]	+

OCA at 19:15, 10 March 2021

2021-03-10T19:15:05Z

←Older revision		Revision as of 19:15, 10 March 2021
Line 1:		Line 1:

	==Crystal Structure of human RanGAP1-Ubc9-D127S==		==Crystal Structure of human RanGAP1-Ubc9-D127S==
-	<StructureSection load='2grr' size='340' side='right' caption='[[2grr]], [[Resolution\|resolution]] 1.30Å' scene=''>	+	<StructureSection load='2grr' size='340' side='right'caption='[[2grr]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2grr]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2GRR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2grr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GRR FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2grn\|2grn]], [[2gro\|2gro]], [[2grp\|2grp]], [[2grq\|2grq]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2grn\|2grn]], [[2gro\|2gro]], [[2grp\|2grp]], [[2grq\|2grq]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2I, UBC9, UBCE9 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RANGAP1 ([~~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">UBE2I, UBC9, UBCE9 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RANGAP1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </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=2grr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2grr OCA], [~~http~~://pdbe.org/2grr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2grr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2grr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2grr 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=2grr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2grr OCA], [https://pdbe.org/2grr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2grr RCSB], [https://www.ebi.ac.uk/pdbsum/2grr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2grr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/UBC9_HUMAN UBC9_HUMAN]] Accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3 and SUMO4 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2 or CBX4. Can catalyze the formation of poly-SUMO chains. Necessary for sumoylation of FOXL2 and KAT5. Essential for nuclear architecture and chromosome segregation.<ref>PMID:8668529</ref> <ref>PMID:11451954</ref> <ref>PMID:15809060</ref> <ref>PMID:19744555</ref> <ref>PMID:19638400</ref> <ref>PMID:17466333</ref> <ref>PMID:20077568</ref>	+	[[https://www.uniprot.org/uniprot/UBC9_HUMAN UBC9_HUMAN]] Accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3 and SUMO4 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2 or CBX4. Can catalyze the formation of poly-SUMO chains. Necessary for sumoylation of FOXL2 and KAT5. Essential for nuclear architecture and chromosome segregation.<ref>PMID:8668529</ref> <ref>PMID:11451954</ref> <ref>PMID:15809060</ref> <ref>PMID:19744555</ref> <ref>PMID:19638400</ref> <ref>PMID:17466333</ref> <ref>PMID:20077568</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gr/2grr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gr/2grr_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>
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	</div>		</div>
	<div class="pdbe-citations 2grr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2grr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[SUMO conjugating enzyme Ubc9\|SUMO conjugating enzyme Ubc9]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]
	[[Category: Lima, C D]]		[[Category: Lima, C D]]

OCA at 07:59, 18 October 2017

2017-10-18T07:59:06Z

←Older revision		Revision as of 07:59, 18 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of human RanGAP1-Ubc9-D127S==		==Crystal Structure of human RanGAP1-Ubc9-D127S==
	<StructureSection load='2grr' size='340' side='right' caption='[[2grr]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='2grr' size='340' side='right' caption='[[2grr]], [[Resolution\|resolution]] 1.30Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2I, UBC9, UBCE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RANGAP1 ([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">UBE2I, UBC9, UBCE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RANGAP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </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=2grr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2grr OCA], [http://pdbe.org/2grr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2grr RCSB], [http://www.ebi.ac.uk/pdbsum/2grr 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=2grr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2grr OCA], [http://pdbe.org/2grr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2grr RCSB], [http://www.ebi.ac.uk/pdbsum/2grr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2grr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=2grr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2grr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2grr" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[SUMO conjugating enzyme Ubc9\|SUMO conjugating enzyme Ubc9]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:36, 11 September 2015

2015-09-11T13:36:15Z

←Older revision		Revision as of 13:36, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2grr' size='340' side='right' caption='[[2grr]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='2grr' size='340' side='right' caption='[[2grr]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2grr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GRR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2grr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GRR FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2grn\|2grn]], [[2gro\|2gro]], [[2grp\|2grp]], [[2grq\|2grq]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2grn\|2grn]], [[2gro\|2gro]], [[2grp\|2grp]], [[2grq\|2grq]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2I, UBC9, UBCE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~]), RANGAP1 ([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">UBE2I, UBC9, UBCE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RANGAP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </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=2grr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2grr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2grr RCSB], [http://www.ebi.ac.uk/pdbsum/2grr 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=2grr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2grr OCA], [http://pdbe.org/2grr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2grr RCSB], [http://www.ebi.ac.uk/pdbsum/2grr PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UBC9_HUMAN UBC9_HUMAN]] Accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3 and SUMO4 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2 or CBX4. Can catalyze the formation of poly-SUMO chains. Necessary for sumoylation of FOXL2 and KAT5. Essential for nuclear architecture and chromosome segregation.<ref>PMID:8668529</ref> <ref>PMID:11451954</ref> <ref>PMID:15809060</ref> <ref>PMID:19744555</ref> <ref>PMID:19638400</ref> <ref>PMID:17466333</ref> <ref>PMID:20077568</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 26:		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 2grr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]
	[[Category: Lima, C D]]		[[Category: Lima, C D]]

OCA at 17:10, 25 December 2014

2014-12-25T17:10:08Z

←Older revision		Revision as of 17:10, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2grr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GRR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2grr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GRR FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2grn\|2grn]], [[2gro\|2gro]], [[2grp\|2grp]], [[2grq\|2grq]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2grn\|2grn]], [[2gro\|2gro]], [[2grp\|2grp]], [[2grq\|2grq]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2I, UBC9, UBCE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RANGAP1 ([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">UBE2I, UBC9, UBCE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RANGAP1 ([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>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span></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=2grr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2grr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2grr RCSB], [http://www.ebi.ac.uk/pdbsum/2grr 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=2grr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2grr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2grr RCSB], [http://www.ebi.ac.uk/pdbsum/2grr PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]
-	[[Category: Lima, C D.]]	+	[[Category: Lima, C D]]
-	[[Category: Yunus, A A.]]	+	[[Category: Yunus, A A]]
	[[Category: Conjugation]]		[[Category: Conjugation]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 04:30, 29 September 2014

2014-09-29T04:30:27Z

←Older revision		Revision as of 04:30, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2grr.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of human RanGAP1-Ubc9-D127S==
		+	<StructureSection load='2grr' size='340' side='right' caption='[[2grr]], [[Resolution\|resolution]] 1.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2grr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GRR FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2grn\|2grn]], [[2gro\|2gro]], [[2grp\|2grp]], [[2grq\|2grq]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2I, UBC9, UBCE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RANGAP1 ([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>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span></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=2grr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2grr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2grr RCSB], [http://www.ebi.ac.uk/pdbsum/2grr 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/gr/2grr_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 ==
		+	E2 conjugating proteins that transfer ubiquitin and ubiquitin-like modifiers to substrate lysine residues must first activate the lysine nucleophile for conjugation. Genetic complementation revealed three side chains of the E2 Ubc9 that were crucial for normal growth. Kinetic analysis revealed modest binding defects but substantially lowered catalytic rates for these mutant alleles with respect to wild-type Ubc9. X-ray structures for wild-type and mutant human Ubc9-RanGAP1 complexes showed partial loss of contacts to the substrate lysine in mutant complexes. Computational analysis predicted pK perturbations for the substrate lysine, and Ubc9 mutations weakened pK suppression through improper side chain coordination. Biochemical studies with p53, RanGAP1 and the Nup358/RanBP2 E3 were used to determine rate constants and pK values, confirming both structural and computational predictions. It seems that Ubc9 uses an indirect mechanism to activate lysine for conjugation that may be conserved among E2 family members.

-	~~{{STRUCTURE_2grr\| PDB=2grr \| SCENE= }}~~	+	Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway.,Yunus AA, Lima CD Nat Struct Mol Biol. 2006 Jun;13(6):491-9. Epub 2006 May 28. PMID:16732283<ref>PMID:16732283</ref>

-	~~===Crystal Structure~~ of ~~human RanGAP1-Ubc9-D127S===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16732283}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2grr]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA].~~	+

	==See Also==		==See Also==
	*[[SUMO conjugating enzyme Ubc9\|SUMO conjugating enzyme Ubc9]]		*[[SUMO conjugating enzyme Ubc9\|SUMO conjugating enzyme Ubc9]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016732283<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]

OCA at 19:17, 20 October 2012

2012-10-20T19:17:30Z

←Older revision		Revision as of 19:17, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2grr]] is a 2 chain structure ~~of [[SUMO conjugating enzyme Ubc9]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA].	+	[[2grr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA].

	==See Also==		==See Also==

OCA: Protected "2grr" [edit=sysop:move=sysop]

2012-07-27T06:52:12Z

Protected "2grr" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:52, 27 July 2012

OCA at 06:52, 27 July 2012

2012-07-27T06:52:11Z

←Older revision		Revision as of 06:52, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2grr.png\|left\|200px]]		[[Image:2grr.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2grr", 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_2grr\| PDB=2grr \| SCENE= }}		{{STRUCTURE_2grr\| PDB=2grr \| SCENE= }}

	===Crystal Structure of human RanGAP1-Ubc9-D127S===		===Crystal Structure of human RanGAP1-Ubc9-D127S===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16732283}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16732283 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_16732283}}		{{ABSTRACT_PUBMED_16732283}}

	==About this Structure==		==About this Structure==
-	~~2GRR~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA].	+	[[2grr]] is a 2 chain structure of [[SUMO conjugating enzyme Ubc9]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA].
		+
		+	==See Also==
		+	*[[SUMO conjugating enzyme Ubc9\|SUMO conjugating enzyme Ubc9]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16732283~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016732283</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]
Line 29:		Line 20:
	[[Category: Yunus, A A.]]		[[Category: Yunus, A A.]]
	[[Category: Conjugation]]		[[Category: Conjugation]]
		+	[[Category: Ligase]]
	[[Category: Small ubiquitin like modifer]]		[[Category: Small ubiquitin like modifer]]
	[[Category: Smt3]]		[[Category: Smt3]]
	[[Category: Ubiquitin]]		[[Category: Ubiquitin]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 23:35:08 2009''

OCA at 21:35, 17 February 2009

2009-02-17T21:35:12Z

←Older revision		Revision as of 21:35, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2GRR is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA].	+	2GRR is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GRR OCA].

	==Reference==		==Reference==
-	~~Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway., Yunus AA, Lima CD, Nat Struct Mol Biol. 2006 Jun;13(6):491-9. Epub 2006 May 28.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16732283 16732283]~~	+	<ref group="xtra">PMID:16732283</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Protein complex]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]
	[[Category: Lima, C D.]]		[[Category: Lima, C D.]]
Line 34:		Line 33:
	[[Category: Ubiquitin]]		[[Category: Ubiquitin]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 06~~:59:~~20 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 23:35:08 2009''