3ptf - Revision history

OCA at 10:01, 6 September 2023

2023-09-06T10:01:11Z

←Older revision		Revision as of 10:01, 6 September 2023
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	<StructureSection load='3ptf' size='340' side='right'caption='[[3ptf]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3ptf' size='340' side='right'caption='[[3ptf]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ptf]] is a 4 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=3PTF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PTF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ptf]] is a 4 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=3PTF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PTF FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>SFT, UBC5A, UBCH5, UBCH5A, UBE2D1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=9606 HUMAN]), Ubiquitin ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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]] 2.7Å</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=3ptf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ptf OCA], [https://pdbe.org/3ptf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ptf RCSB], [https://www.ebi.ac.uk/pdbsum/3ptf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ptf 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=3ptf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ptf OCA], [https://pdbe.org/3ptf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ptf RCSB], [https://www.ebi.ac.uk/pdbsum/3ptf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ptf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/UB2D1_HUMAN UB2D1_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and auto-ubiquitination of STUB1, TRAF6 and TRIM63/MURF1. Ubiquitinates STUB1-associated HSP90AB1 in vitro. Lacks inherent specificity for any particular lysine residue of ubiquitin. Essential for viral activation of IRF3. Mediates polyubiquitination of CYP3A4.<ref>PMID:18042044</ref> <ref>PMID:18359941</ref> <ref>PMID:19103148</ref> <ref>PMID:19854139</ref> <ref>PMID:20061386</ref> [[https://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>	+	[https://www.uniprot.org/uniprot/UB2D1_HUMAN UB2D1_HUMAN] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and auto-ubiquitination of STUB1, TRAF6 and TRIM63/MURF1. Ubiquitinates STUB1-associated HSP90AB1 in vitro. Lacks inherent specificity for any particular lysine residue of ubiquitin. Essential for viral activation of IRF3. Mediates polyubiquitination of CYP3A4.<ref>PMID:18042044</ref> <ref>PMID:18359941</ref> <ref>PMID:19103148</ref> <ref>PMID:19854139</ref> <ref>PMID:20061386</ref>
	<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: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ubiquitin--protein ligase]]~~	+	[[Category: Bosanac I]]
-	[[Category: Bosanac, I]]	+	[[Category: Hymowitz SG]]
-	[[Category: Hymowitz~~, S G]]~~	+
-	~~[[Category: Alpha/beta]]~~	+
-	~~[[Category: E2]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Protein-protein complex]]~~	+
-	~~[[Category: Ubiquitin]]~~	+
-	~~[[Category: Ubiquitin conjugating enzyme~~]]	+

OCA at 08:54, 25 May 2022

2022-05-25T08:54:13Z

←Older revision		Revision as of 08:54, 25 May 2022
Line 1:		Line 1:

	==X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin==		==X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin==
-	<StructureSection load='3ptf' size='340' side='right' caption='[[3ptf]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='3ptf' size='340' side='right'caption='[[3ptf]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ptf]] is a 4 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=3PTF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3PTF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ptf]] is a 4 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=3PTF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PTF FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFT, UBC5A, UBCH5, UBCH5A, UBE2D1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), Ubiquitin ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFT, UBC5A, UBCH5, UBCH5A, UBE2D1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), Ubiquitin ([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=3ptf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ptf OCA], [~~http~~://pdbe.org/3ptf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ptf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ptf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ptf 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=3ptf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ptf OCA], [https://pdbe.org/3ptf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ptf RCSB], [https://www.ebi.ac.uk/pdbsum/3ptf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ptf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/UB2D1_HUMAN UB2D1_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and auto-ubiquitination of STUB1, TRAF6 and TRIM63/MURF1. Ubiquitinates STUB1-associated HSP90AB1 in vitro. Lacks inherent specificity for any particular lysine residue of ubiquitin. Essential for viral activation of IRF3. Mediates polyubiquitination of CYP3A4.<ref>PMID:18042044</ref> <ref>PMID:18359941</ref> <ref>PMID:19103148</ref> <ref>PMID:19854139</ref> <ref>PMID:20061386</ref> [[~~http~~://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>	+	[[https://www.uniprot.org/uniprot/UB2D1_HUMAN UB2D1_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and auto-ubiquitination of STUB1, TRAF6 and TRIM63/MURF1. Ubiquitinates STUB1-associated HSP90AB1 in vitro. Lacks inherent specificity for any particular lysine residue of ubiquitin. Essential for viral activation of IRF3. Mediates polyubiquitination of CYP3A4.<ref>PMID:18042044</ref> <ref>PMID:18359941</ref> <ref>PMID:19103148</ref> <ref>PMID:19854139</ref> <ref>PMID:20061386</ref> [[https://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Ubiquitin\|Ubiquitin]]
	*[[Ubiquitin conjugating enzyme\|Ubiquitin conjugating enzyme]]		*[[Ubiquitin conjugating enzyme\|Ubiquitin conjugating enzyme]]
		+	*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
		+	*[[3D structures of ubiquitin conjugating enzyme\|3D structures of ubiquitin conjugating enzyme]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]
	[[Category: Bosanac, I]]		[[Category: Bosanac, I]]

OCA at 16:19, 4 August 2016

2016-08-04T16:19:12Z

←Older revision		Revision as of 16:19, 4 August 2016
Line 1:		Line 1:
		+
	==X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin==		==X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin==
	<StructureSection load='3ptf' size='340' side='right' caption='[[3ptf]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3ptf' size='340' side='right' caption='[[3ptf]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ptf]] is a 4 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=3PTF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PTF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ptf]] is a 4 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=3PTF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PTF FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFT, UBC5A, UBCH5, UBCH5A, UBE2D1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~]), Ubiquitin ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFT, UBC5A, UBCH5, UBCH5A, UBE2D1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), Ubiquitin ([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=3ptf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ptf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ptf RCSB], [http://www.ebi.ac.uk/pdbsum/3ptf 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=3ptf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ptf OCA], [http://pdbe.org/3ptf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ptf RCSB], [http://www.ebi.ac.uk/pdbsum/3ptf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ptf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 3ptf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]
	[[Category: Bosanac, I]]		[[Category: Bosanac, I]]

OCA at 10:56, 25 December 2014

2014-12-25T10:56:27Z

←Older revision		Revision as of 10:56, 25 December 2014
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	<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=3ptf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ptf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ptf RCSB], [http://www.ebi.ac.uk/pdbsum/3ptf 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=3ptf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ptf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ptf RCSB], [http://www.ebi.ac.uk/pdbsum/3ptf PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UB2D1_HUMAN UB2D1_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and auto-ubiquitination of STUB1, TRAF6 and TRIM63/MURF1. Ubiquitinates STUB1-associated HSP90AB1 in vitro. Lacks inherent specificity for any particular lysine residue of ubiquitin. Essential for viral activation of IRF3. Mediates polyubiquitination of CYP3A4.<ref>PMID:18042044</ref> <ref>PMID:18359941</ref> <ref>PMID:19103148</ref> <ref>PMID:19854139</ref> <ref>PMID:20061386</ref> [[http://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:45, 19 December 2014

2014-12-19T10:45:03Z

←Older revision		Revision as of 10:45, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3ptf\| PDB=3ptf \| SCENE= }}~~	+	==X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin==
-	===X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin===	+	<StructureSection load='3ptf' size='340' side='right' caption='[[3ptf]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21396940}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ptf]] is a 4 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=3PTF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PTF FirstGlance]. <br>
		+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFT, UBC5A, UBCH5, UBCH5A, UBE2D1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), Ubiquitin ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3ptf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ptf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ptf RCSB], [http://www.ebi.ac.uk/pdbsum/3ptf PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ubiquitination refers to the covalent addition of ubiquitin (Ub) to substrate proteins or other Ub molecules via the sequential action of three enzymes (E1, E2, and E3). Recent advances in mass spectrometry proteomics have made it possible to identify and quantify Ub linkages in biochemical and cellular systems. We used these tools to probe the mechanisms controlling linkage specificity for UbcH5A. UbcH5A is a promiscuous E2 enzyme with an innate preference for forming polyubiquitin chains through lysine 11 (K11), lysine 48 (K48), and lysine 63 (K63) of Ub. We present the crystal structure of a noncovalent complex between Ub and UbcH5A. This structure reveals an interaction between the Ub surface flanking K11 and residues adjacent to the E2 catalytic cysteine and suggests a possible role for this surface in formation of K11 linkages. Structure-guided mutagenesis, in vitro ubiquitination and quantitative mass spectrometry have been used to characterize the ability of residues in the vicinity of the E2 active site to direct synthesis of K11- and K63-linked polyubiquitin. Mutation of critical residues in the interface modulated the linkage specificity of UbcH5A, resulting in generation of more K63-linked chains at the expense of K11-linkage synthesis. This study provides direct evidence that the linkage specificity of E2 enzymes may be altered through active-site mutagenesis.

-	~~==Function==~~	+	Modulation of K11-Linkage Formation by Variable Loop Residues within UbcH5A.,Bosanac I, Phu L, Pan B, Zilberleyb I, Maurer B, Dixit VM, Hymowitz SG, Kirkpatrick DS J Mol Biol. 2011 May 6;408(3):420-31. Epub 2011 Mar 10. PMID:21396940<ref>PMID:21396940</ref>
-	[[http://www.uniprot.org/uniprot/UB2D1_HUMAN UB2D1_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of ~~short~~-~~lived and abnormal proteins~~. ~~Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and auto-ubiquitination of STUB1~~, TRAF6 and TRIM63/MURF1. Ubiquitinates STUB1-associated HSP90AB1 in vitro. Lacks inherent specificity for any particular lysine residue of ubiquitin. Essential for viral activation of IRF3. Mediates polyubiquitination of CYP3A4.<ref>PMID:18042044</ref> <ref>PMID:18359941</ref> <ref>PMID:19103148</ref> <ref>PMID:19854139</ref> <ref>PMID:20061386</ref> [[http://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, ~~or free (unanchored). When covalently bound~~, ~~it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin)~~, a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, ~~when attached to a target protein~~, ~~have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-~~6~~-linked may be involved in DNA repair~~; ~~Lys-11-linked is involved in ERAD~~ (~~endoplasmic reticulum-associated degradation~~) ~~and in cell~~-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. ~~Linear polymer chains formed via attachment by the initiator Met lead to cell signaling~~. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:~~16543144</ref>~~ <ref>PMID:~~19754430~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3ptf]] is~~ a ~~4 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=3PTF OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:021396940</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Ubiquitin\|Ubiquitin]]
		+	*[[Ubiquitin conjugating enzyme\|Ubiquitin conjugating enzyme]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]
-	[[Category: Bosanac, I.]]	+	[[Category: Bosanac, I]]
-	[[Category: Hymowitz, S G.]]	+	[[Category: Hymowitz, S G]]
	[[Category: Alpha/beta]]		[[Category: Alpha/beta]]
	[[Category: E2]]		[[Category: E2]]

OCA at 08:12, 8 May 2013

2013-05-08T08:12:53Z

←Older revision		Revision as of 08:12, 8 May 2013
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-	[[Image:3ptf.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ptf", 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_3ptf\| PDB=3ptf \| SCENE= }}		{{STRUCTURE_3ptf\| PDB=3ptf \| SCENE= }}
-
	===X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin===		===X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin===
		+	{{ABSTRACT_PUBMED_21396940}}

-		+	==Function==
-	<!--	+	[[http://www.uniprot.org/uniprot/UB2D1_HUMAN UB2D1_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and auto-ubiquitination of STUB1, TRAF6 and TRIM63/MURF1. Ubiquitinates STUB1-associated HSP90AB1 in vitro. Lacks inherent specificity for any particular lysine residue of ubiquitin. Essential for viral activation of IRF3. Mediates polyubiquitination of CYP3A4.<ref>PMID:18042044</ref> <ref>PMID:18359941</ref> <ref>PMID:19103148</ref> <ref>PMID:19854139</ref> <ref>PMID:20061386</ref> [[http://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21396940}}, adds~~ the ~~Publication Abstract to~~ the ~~page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov~~), ~~where 21396940~~ is the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_21396940}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:021396940</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021396940</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Ubiquitin--protein ligase]]		[[Category: Ubiquitin--protein ligase]]
	[[Category: Bosanac, I.]]		[[Category: Bosanac, I.]]
	[[Category: Hymowitz, S G.]]		[[Category: Hymowitz, S G.]]
		+	[[Category: Alpha/beta]]
		+	[[Category: E2]]
		+	[[Category: Ligase]]
		+	[[Category: Protein-protein complex]]
		+	[[Category: Ubiquitin]]
		+	[[Category: Ubiquitin conjugating enzyme]]

OCA: Protected "3ptf" [edit=sysop:move=sysop]

2011-05-12T04:40:19Z

Protected "3ptf" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:40, 12 May 2011

OCA at 04:40, 12 May 2011

2011-05-12T04:40:16Z

←Older revision		Revision as of 04:40, 12 May 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3ptf.jpg\|left\|200px]]

-	The ~~entry 3ptf~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3ptf", 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_3ptf\| PDB=3ptf \| SCENE= }}

-	~~Authors: Bosanac, I., Hymowitz, S.G.~~	+	===X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin===

-	Description: X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Dec 15 08~~:25:~~20 2010''~~	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21396940}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21396940 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21396940}}
		+
		+	==About this Structure==
		+	[[3ptf]] is a 4 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=3PTF OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021396940</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Ubiquitin--protein ligase]]
		+	[[Category: Bosanac, I.]]
		+	[[Category: Hymowitz, S G.]]

OCA at 05:13, 15 December 2010

2010-12-15T05:13:00Z

←Older revision		Revision as of 05:13, 15 December 2010
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	The entry 3ptf is ON HOLD		The entry 3ptf is ON HOLD

-	Authors: Bosanac, I~~., Phu, L., Pan, B., Zilberleyb, Z., Maurer, B., Dixit, V.M~~., Hymowitz, S.G~~., Kirkpatrick, D.S~~.	+	Authors: Bosanac, I., Hymowitz, S.G.

	Description: X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin		Description: X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec ~~8 11~~:33:53 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 15 08:25:20 2010''

OCA: New page: '''Unreleased structure''' The entry 3ptf is ON HOLD Authors: Bosanac, I., Phu, L., Pan, B., Zilberleyb, Z., Maurer, B., Dixit, V.M., Hymowitz, S.G., Kirkpatrick, D.S. Description: X-r...

2010-12-08T08:21:50Z

New page: '''Unreleased structure''' The entry 3ptf is ON HOLD Authors: Bosanac, I., Phu, L., Pan, B., Zilberleyb, Z., Maurer, B., Dixit, V.M., Hymowitz, S.G., Kirkpatrick, D.S. Description: X-r...

New page

'''Unreleased structure'''

The entry 3ptf is ON HOLD

Authors: Bosanac, I., Phu, L., Pan, B., Zilberleyb, Z., Maurer, B., Dixit, V.M., Hymowitz, S.G., Kirkpatrick, D.S.

Description: X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 8 11:33:53 2010''