1ify - Revision history

OCA at 08:34, 22 May 2024

2024-05-22T08:34:50Z

← Older revision		Revision as of 08:34, 22 May 2024
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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=1ify 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=1ify ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signaling via protein kinases. The human homologue of yeast Rad23A (HHR23A) is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of HHR23A UBA(2) showed that the domain forms a compact three-helix bundle. We report the structure of the internal UBA(1) domain of HHR23A. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch. The structural similarity between UBA(1) and UBA(2), in spite of their low level of sequence conservation, leads us to conclude that the structural variability of UBA domains in general is likely to be rather small. On the basis of the structural similarities as well as analysis of sequence conservation, we predict that this hydrophobic surface patch is a common protein-interacting surface present in diverse UBA domains. Furthermore, accumulating evidence that ubiquitin binds to UBA domains leads us to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin. Detailed comparison of the structures of the two UBA domains, combined with previous mutagenesis studies, indicates that the binding site of HIV-1 Vpr on UBA(2) does not completely overlap the ubiquitin binding site.

			Solution structures of UBA domains reveal a conserved hydrophobic surface for protein-protein interactions.,Mueller TD, Feigon J J Mol Biol. 2002 Jun 21;319(5):1243-55. PMID:12079361<ref>PMID:12079361</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 1ify" style="background-color:#fffaf0;"></div>

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

OCA at 07:46, 3 April 2024

2024-04-03T07:46:55Z

← Older revision		Revision as of 07:46, 3 April 2024
Line 1:		Line 1:

	==Solution Structure of the Internal UBA Domain of HHR23A==		==Solution Structure of the Internal UBA Domain of HHR23A==
	<StructureSection load='1ify' size='340' side='right'caption='[[1ify~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>		<StructureSection load='1ify' size='340' side='right'caption='[[1ify]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ify]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IFY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ify]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IFY 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;'>[[1dv0\|1dv0]], [[1f4i\|1f4i]]</div~~></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ify OCA], [https://pdbe.org/1ify PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ify RCSB], [https://www.ebi.ac.uk/pdbsum/1ify PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ify 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=1ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ify OCA], [https://pdbe.org/1ify PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ify RCSB], [https://www.ebi.ac.uk/pdbsum/1ify PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ify ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/RD23A_HUMAN RD23A_HUMAN]] Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in nucleotide excision repair and is thought to be functional equivalent for RAD23B in global genome nucleotide excision repair (GG-NER) by association with XPC. In vitro, the XPC:RAD23A dimer has NER activity. Can stabilize XPC.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in vpr-dependent replication of HIV-1 in non-proliferating cells and primary macrophages. Required for the association of HIV-1 vpr with the host proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref>		[https://www.uniprot.org/uniprot/RD23A_HUMAN RD23A_HUMAN] Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in nucleotide excision repair and is thought to be functional equivalent for RAD23B in global genome nucleotide excision repair (GG-NER) by association with XPC. In vitro, the XPC:RAD23A dimer has NER activity. Can stabilize XPC.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in vpr-dependent replication of HIV-1 in non-proliferating cells and primary macrophages. Required for the association of HIV-1 vpr with the host proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</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=1ify 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=1ify ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signaling via protein kinases. The human homologue of yeast Rad23A (HHR23A) is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of HHR23A UBA(2) showed that the domain forms a compact three-helix bundle. We report the structure of the internal UBA(1) domain of HHR23A. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch. The structural similarity between UBA(1) and UBA(2), in spite of their low level of sequence conservation, leads us to conclude that the structural variability of UBA domains in general is likely to be rather small. On the basis of the structural similarities as well as analysis of sequence conservation, we predict that this hydrophobic surface patch is a common protein-interacting surface present in diverse UBA domains. Furthermore, accumulating evidence that ubiquitin binds to UBA domains leads us to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin. Detailed comparison of the structures of the two UBA domains, combined with previous mutagenesis studies, indicates that the binding site of HIV-1 Vpr on UBA(2) does not completely overlap the ubiquitin binding site.

	Solution structures of UBA domains reveal a conserved hydrophobic surface for protein-protein interactions.,Mueller TD, Feigon J J Mol Biol. 2002 Jun 21;319(5):1243-55. PMID:12079361<ref>PMID:12079361</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 1ify" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[UV excision repair protein\|UV excision repair protein]]		*[[UV excision repair protein 3D structures\|UV excision repair protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Feigon, J]]		[[Category: Feigon J]]
	[[Category: Mueller~~, T D]]~~		[[Category: Mueller TD]]
	~~[[Category: Dna binding protein]]~~
	~~[[Category: Uba domain]]~~
	~~[[Category: Ubiquitin associated domain]]~~
	~~[[Category: Ubiquitin proteosome pathway~~]]

OCA at 11:00, 4 August 2021

2021-08-04T11:00:23Z

← Older revision		Revision as of 11:00, 4 August 2021
Line 3:		Line 3:
	<StructureSection load='1ify' size='340' side='right'caption='[[1ify]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1ify' size='340' side='right'caption='[[1ify]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ify]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1IFY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ify]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IFY FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dv0\|1dv0]], [[1f4i\|1f4i]]</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;'>[[1dv0\|1dv0]], [[1f4i\|1f4i]]</div></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=1ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ify OCA], [~~http~~://pdbe.org/1ify PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ify RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ify PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ify 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=1ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ify OCA], [https://pdbe.org/1ify PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ify RCSB], [https://www.ebi.ac.uk/pdbsum/1ify PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ify ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/RD23A_HUMAN RD23A_HUMAN]] Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in nucleotide excision repair and is thought to be functional equivalent for RAD23B in global genome nucleotide excision repair (GG-NER) by association with XPC. In vitro, the XPC:RAD23A dimer has NER activity. Can stabilize XPC.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in vpr-dependent replication of HIV-1 in non-proliferating cells and primary macrophages. Required for the association of HIV-1 vpr with the host proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref>		[[https://www.uniprot.org/uniprot/RD23A_HUMAN RD23A_HUMAN]] Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in nucleotide excision repair and is thought to be functional equivalent for RAD23B in global genome nucleotide excision repair (GG-NER) by association with XPC. In vitro, the XPC:RAD23A dimer has NER activity. Can stabilize XPC.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in vpr-dependent replication of HIV-1 in non-proliferating cells and primary macrophages. Required for the association of HIV-1 vpr with the host proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:17, 30 October 2019

2019-10-30T10:17:53Z

← Older revision		Revision as of 10:17, 30 October 2019
Line 1:		Line 1:

	==Solution Structure of the Internal UBA Domain of HHR23A==		==Solution Structure of the Internal UBA Domain of HHR23A==
	<StructureSection load='1ify' size='340' side='right' caption='[[1ify]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1ify' size='340' side='right'caption='[[1ify]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ify]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ify]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFY FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 1ify" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ify" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[UV excision repair protein\|UV excision repair protein]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Feigon, J]]		[[Category: Feigon, J]]
	[[Category: Mueller, T D]]		[[Category: Mueller, T D]]

OCA at 09:18, 10 January 2018

2018-01-10T09:18:59Z

← Older revision		Revision as of 09:18, 10 January 2018
Line 1:		Line 1:

	==Solution Structure of the Internal UBA Domain of HHR23A==		==Solution Structure of the Internal UBA Domain of HHR23A==
	<StructureSection load='1ify' size='340' side='right' caption='[[1ify]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1ify' size='340' side='right' caption='[[1ify]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1ify]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ify]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFY FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dv0\|1dv0]], [[1f4i\|1f4i]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dv0\|1dv0]], [[1f4i\|1f4i]]</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=1ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ify OCA], [http://pdbe.org/1ify PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ify RCSB], [http://www.ebi.ac.uk/pdbsum/1ify 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=1ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ify OCA], [http://pdbe.org/1ify PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ify RCSB], [http://www.ebi.ac.uk/pdbsum/1ify PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ify ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/if/1ify_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/if/1ify_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 17:01, 8 February 2016

2016-02-08T17:01:07Z

← Older revision		Revision as of 17:01, 8 February 2016
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	<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=1ify ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:37, 10 September 2015

2015-09-10T13:37:46Z

← Older revision		Revision as of 13:37, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1ify' size='340' side='right' caption='[[1ify]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1ify' size='340' side='right' caption='[[1ify]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ify]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ify]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFY FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dv0\|1dv0]], [[1f4i\|1f4i]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dv0\|1dv0]], [[1f4i\|1f4i]]</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=1ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ify OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ify RCSB], [http://www.ebi.ac.uk/pdbsum/1ify 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=1ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ify OCA], [http://pdbe.org/1ify PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ify RCSB], [http://www.ebi.ac.uk/pdbsum/1ify PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 1ify" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Feigon, J]]		[[Category: Feigon, J]]
	[[Category: Mueller, T D]]		[[Category: Mueller, T D]]

OCA at 00:51, 25 December 2014

2014-12-25T00:51:27Z

← Older revision		Revision as of 00:51, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ify]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ify]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFY FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dv0\|1dv0]], [[1f4i\|1f4i]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dv0\|1dv0]], [[1f4i\|1f4i]]</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=1ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ify OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ify RCSB], [http://www.ebi.ac.uk/pdbsum/1ify 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=1ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ify OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ify RCSB], [http://www.ebi.ac.uk/pdbsum/1ify PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/RD23A_HUMAN RD23A_HUMAN]] Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in nucleotide excision repair and is thought to be functional equivalent for RAD23B in global genome nucleotide excision repair (GG-NER) by association with XPC. In vitro, the XPC:RAD23A dimer has NER activity. Can stabilize XPC.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in vpr-dependent replication of HIV-1 in non-proliferating cells and primary macrophages. Required for the association of HIV-1 vpr with the host proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Feigon, J.]]		[[Category: Feigon, J]]
	[[Category: Mueller, T D.]]		[[Category: Mueller, T D]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Uba domain]]		[[Category: Uba domain]]
	[[Category: Ubiquitin associated domain]]		[[Category: Ubiquitin associated domain]]
	[[Category: Ubiquitin proteosome pathway]]		[[Category: Ubiquitin proteosome pathway]]

OCA at 12:03, 28 September 2014

2014-09-28T12:03:24Z

← Older revision		Revision as of 12:03, 28 September 2014
Line 1:		Line 1:
	[[Image:~~1ify~~.~~png~~\|~~left~~\|~~200px~~]]		==Solution Structure of the Internal UBA Domain of HHR23A==
			<StructureSection load='1ify' size='340' side='right' caption='[[1ify]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[1ify]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFY FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dv0\|1dv0]], [[1f4i\|1f4i]]</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=1ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ify OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ify RCSB], [http://www.ebi.ac.uk/pdbsum/1ify 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/if/1ify_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 ==
			UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signaling via protein kinases. The human homologue of yeast Rad23A (HHR23A) is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of HHR23A UBA(2) showed that the domain forms a compact three-helix bundle. We report the structure of the internal UBA(1) domain of HHR23A. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch. The structural similarity between UBA(1) and UBA(2), in spite of their low level of sequence conservation, leads us to conclude that the structural variability of UBA domains in general is likely to be rather small. On the basis of the structural similarities as well as analysis of sequence conservation, we predict that this hydrophobic surface patch is a common protein-interacting surface present in diverse UBA domains. Furthermore, accumulating evidence that ubiquitin binds to UBA domains leads us to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin. Detailed comparison of the structures of the two UBA domains, combined with previous mutagenesis studies, indicates that the binding site of HIV-1 Vpr on UBA(2) does not completely overlap the ubiquitin binding site.

	~~{{STRUCTURE_1ify\| PDB=1ify \| SCENE= }}~~		Solution structures of UBA domains reveal a conserved hydrophobic surface for protein-protein interactions.,Mueller TD, Feigon J J Mol Biol. 2002 Jun 21;319(5):1243-55. PMID:12079361<ref>PMID:12079361</ref>

	~~===Solution Structure~~ of the ~~Internal UBA Domain of HHR23A===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_12079361}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[1ify]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1IFY OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:012079361<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Feigon, J.]]		[[Category: Feigon, J.]]

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

2012-11-28T14:54:23Z

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

← Older revision	Revision as of 14:54, 28 November 2012
(No difference)