5ekg - Revision history

OCA at 12:28, 6 March 2024

OCA — Wed, 06 Mar 2024 12:28:53 GMT

←Older revision		Revision as of 12:28, 6 March 2024
Line 11:		Line 11:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/ERCC5_HUMAN ERCC5_HUMAN] Single-stranded structure-specific DNA endonuclease involved in DNA excision repair. Makes the 3'incision in DNA nucleotide excision repair (NER). Acts as a cofactor for a DNA glycosylase that removes oxidized pyrimidines from DNA. May also be involved in transcription-coupled repair of this kind of damage, in transcription by RNA polymerase II, and perhaps in other processes too.		[https://www.uniprot.org/uniprot/ERCC5_HUMAN ERCC5_HUMAN] Single-stranded structure-specific DNA endonuclease involved in DNA excision repair. Makes the 3'incision in DNA nucleotide excision repair (NER). Acts as a cofactor for a DNA glycosylase that removes oxidized pyrimidines from DNA. May also be involved in transcription-coupled repair of this kind of damage, in transcription by RNA polymerase II, and perhaps in other processes too.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Xeroderma pigmentosum type G (XPG) proteins are involved in DNA lesion recognition and promotion of nucleotide excision repair (NER). Specific mutations in these proteins may lead to Cockayne syndrome, in which the patients may display severe developmental retardation and neurological abnormalities. No structural information is available for their spacer region or the C-terminal domain, which are important, respectively, for specific NER activity and substrate specificity, and nuclear translocation. Immunofluorescence studies suggested two specific regions of the XPG C-terminus as potential bipartite nuclear localization sequences, which would be responsible for its translocation to the nucleus by the classical nuclear import pathway mediated by importin-alpha (Impalpha). Thus, in order to test these hypotheses and gain insight into the structural basis for the nuclear import process for the XPG protein, we solved the crystal structures of complexes formed by the Impalpha and peptides corresponding to both putative NLS (nuclear localization signal) sequences (XPG1 and XPG2) and performed isothermal titration calorimetry (ITC) assays to determine their binding affinities. Structural experiments confirm the binding of both NLS peptides to Impalpha but, unexpectedly, they bind to the receptor as monopartite NLSs. The ITC assays demonstrated that XPG1 and XPG2 peptides bind to two separate binding-sites, but with high affinity to the major NLS binding-site of the Impalpha, resembling classical monopartite SV40 TAg NLS. The results lead to insights about what distinguishes monopartite and bipartite NLSs, as well as the differential roles of XPG1 and XPG2 NLSs in the nuclear localization of XPG.
-
-	Structural and calorimetric studies demonstrate that Xeroderma pigmentosum type G (XPG) can be imported to the nucleus by a classical nuclear import pathway via a monopartite NLS sequence.,de Barros AC, Takeda AA, Dreyer TR, Velazquez-Campoy A, Kobe B, Fontes MR J Mol Biol. 2016 Jan 23. pii: S0022-2836(16)00038-3. doi:, 10.1016/j.jmb.2016.01.019. PMID:26812207<ref>PMID:26812207</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5ekg" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Importin 3D structures\|Importin 3D structures]]		*[[Importin 3D structures\|Importin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:31, 5 July 2023

OCA — Wed, 05 Jul 2023 06:31:53 GMT

←Older revision		Revision as of 06:31, 5 July 2023
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	<StructureSection load='5ekg' size='340' side='right'caption='[[5ekg]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5ekg' size='340' side='right'caption='[[5ekg]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ekg]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EKG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5EKG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ekg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EKG FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5ekf\|5ekf]]</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]] 2.8Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">Kpna2, Rch1 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=10090 LK3 transgenic mice])~~</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=5ekg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ekg OCA], [https://pdbe.org/5ekg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ekg RCSB], [https://www.ebi.ac.uk/pdbsum/5ekg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ekg ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5ekg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ekg OCA], [~~http~~://pdbe.org/5ekg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ekg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ekg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ekg ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Disease ==
		+	[https://www.uniprot.org/uniprot/ERCC5_HUMAN ERCC5_HUMAN] Xeroderma pigmentosum complementation group G;COFS syndrome. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~IMA1_MOUSE IMA1_MOUSE~~]~~] Functions~~ in ~~nuclear protein import as an adapter protein for nuclear receptor KPNB1~~. ~~Binds specifically and directly to substrates containing either a simple or bipartite NLS motif. Docking of~~ the ~~importin/substrate complex to the nuclear pore complex~~ (~~NPC~~) ~~is mediated by KPNB1 through binding to nucleoporin FxFG repeats and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism~~. ~~At the nucleoplasmic side of the NPC, Ran binds to importin-beta and the three components separate and importin-alpha and -beta are re-exported~~ from ~~the nucleus to the cytoplasm where GTP hydrolysis releases Ran from importin~~. ~~The directionality of nuclear import is thought to~~ be ~~conferred by an asymmetric distribution~~ of ~~the GTP- and GDP-bound forms~~ of ~~Ran between the cytoplasm~~ and ~~nucleus~~.	+	[https://www.uniprot.org/uniprot/ERCC5_HUMAN ERCC5_HUMAN] Single-stranded structure-specific DNA endonuclease involved in DNA excision repair. Makes the 3'incision in DNA nucleotide excision repair (NER). Acts as a cofactor for a DNA glycosylase that removes oxidized pyrimidines from DNA. May also be involved in transcription-coupled repair of this kind of damage, in transcription by RNA polymerase II, and perhaps in other processes too.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Barros, A C~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Fontes, M R.M~~]]	+	[[Category: Barros AC]]
-	[[Category: ~~Takeda, A A.S~~]]	+	[[Category: Fontes MRM]]
-	[[Category: ~~Dna repair protein]]~~	+	[[Category: Takeda AAS]]
-	~~[[Category: Importin alpha]]~~	+
-	~~[[Category: Nuclear import pathway]]~~	+
-	~~[[Category: Nucleotide excision repair]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Xpg protein~~]]	+

OCA at 07:02, 22 April 2020

OCA — Wed, 22 Apr 2020 07:02:40 GMT

←Older revision		Revision as of 07:02, 22 April 2020
Line 1:		Line 1:

	==Crystallization and X-ray Diffraction Data Collection of Importin-alpha from Mus musculus Complexed with a XPG NLS Peptide, fragment 2==		==Crystallization and X-ray Diffraction Data Collection of Importin-alpha from Mus musculus Complexed with a XPG NLS Peptide, fragment 2==
-	<StructureSection load='5ekg' size='340' side='right' caption='[[5ekg]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5ekg' size='340' side='right'caption='[[5ekg]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ekg]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EKG OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5EKG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ekg]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EKG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EKG FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ekf\|5ekf]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ekf\|5ekf]]</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=5ekg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ekg OCA], [http://pdbe.org/5ekg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ekg RCSB], [http://www.ebi.ac.uk/pdbsum/5ekg PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Kpna2, Rch1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ekg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ekg OCA], [http://pdbe.org/5ekg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ekg RCSB], [http://www.ebi.ac.uk/pdbsum/5ekg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ekg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ekg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ekg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Importin 3D structures\|Importin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Barros, A C]]		[[Category: Barros, A C]]
	[[Category: Fontes, M R.M]]		[[Category: Fontes, M R.M]]

OCA at 08:17, 1 June 2016

OCA — Wed, 01 Jun 2016 08:17:18 GMT

←Older revision		Revision as of 08:17, 1 June 2016
Line 1:		Line 1:
		+
	==Crystallization and X-ray Diffraction Data Collection of Importin-alpha from Mus musculus Complexed with a XPG NLS Peptide, fragment 2==		==Crystallization and X-ray Diffraction Data Collection of Importin-alpha from Mus musculus Complexed with a XPG NLS Peptide, fragment 2==
	<StructureSection load='5ekg' size='340' side='right' caption='[[5ekg]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5ekg' size='340' side='right' caption='[[5ekg]], [[Resolution\|resolution]] 2.80Å' scene=''>

OCA at 17:14, 10 February 2016

OCA — Wed, 10 Feb 2016 17:14:24 GMT

←Older revision		Revision as of 17:14, 10 February 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystallization and X-ray Diffraction Data Collection of Importin-alpha from Mus musculus Complexed with a XPG NLS Peptide, fragment 2==
		+	<StructureSection load='5ekg' size='340' side='right' caption='[[5ekg]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ekg]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EKG FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ekf\|5ekf]]</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=5ekg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ekg OCA], [http://pdbe.org/5ekg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ekg RCSB], [http://www.ebi.ac.uk/pdbsum/5ekg PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/IMA1_MOUSE IMA1_MOUSE]] Functions in nuclear protein import as an adapter protein for nuclear receptor KPNB1. Binds specifically and directly to substrates containing either a simple or bipartite NLS motif. Docking of the importin/substrate complex to the nuclear pore complex (NPC) is mediated by KPNB1 through binding to nucleoporin FxFG repeats and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to importin-beta and the three components separate and importin-alpha and -beta are re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran from importin. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Xeroderma pigmentosum type G (XPG) proteins are involved in DNA lesion recognition and promotion of nucleotide excision repair (NER). Specific mutations in these proteins may lead to Cockayne syndrome, in which the patients may display severe developmental retardation and neurological abnormalities. No structural information is available for their spacer region or the C-terminal domain, which are important, respectively, for specific NER activity and substrate specificity, and nuclear translocation. Immunofluorescence studies suggested two specific regions of the XPG C-terminus as potential bipartite nuclear localization sequences, which would be responsible for its translocation to the nucleus by the classical nuclear import pathway mediated by importin-alpha (Impalpha). Thus, in order to test these hypotheses and gain insight into the structural basis for the nuclear import process for the XPG protein, we solved the crystal structures of complexes formed by the Impalpha and peptides corresponding to both putative NLS (nuclear localization signal) sequences (XPG1 and XPG2) and performed isothermal titration calorimetry (ITC) assays to determine their binding affinities. Structural experiments confirm the binding of both NLS peptides to Impalpha but, unexpectedly, they bind to the receptor as monopartite NLSs. The ITC assays demonstrated that XPG1 and XPG2 peptides bind to two separate binding-sites, but with high affinity to the major NLS binding-site of the Impalpha, resembling classical monopartite SV40 TAg NLS. The results lead to insights about what distinguishes monopartite and bipartite NLSs, as well as the differential roles of XPG1 and XPG2 NLSs in the nuclear localization of XPG.

-	~~The entry 5ekg is ON HOLD until Paper Publication~~	+	Structural and calorimetric studies demonstrate that Xeroderma pigmentosum type G (XPG) can be imported to the nucleus by a classical nuclear import pathway via a monopartite NLS sequence.,de Barros AC, Takeda AA, Dreyer TR, Velazquez-Campoy A, Kobe B, Fontes MR J Mol Biol. 2016 Jan 23. pii: S0022-2836(16)00038-3. doi:, 10.1016/j.jmb.2016.01.019. PMID:26812207<ref>PMID:26812207</ref>

-	~~Authors: Barros~~, ~~A.C., Takeda, A.A~~.S.~~, Fontes, M.R.M~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystallization and X~~-~~ray Diffraction Data Collection of Importin~~-~~alpha from Mus musculus Complexed with a XPG NLS Peptide, fragment 2~~	+	<div class="pdbe-citations 5ekg" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: ~~Barros~~, A.C]]	+	<references/>
-	[[Category: Takeda, A.A.S]]	+	__TOC__
-	[[Category: ~~Fontes, M.R.M~~]]	+	</StructureSection>
		+	[[Category: Barros, A C]]
		+	[[Category: Fontes, M R.M]]
		+	[[Category: Takeda, A A.S]]
		+	[[Category: Dna repair protein]]
		+	[[Category: Importin alpha]]
		+	[[Category: Nuclear import pathway]]
		+	[[Category: Nucleotide excision repair]]
		+	[[Category: Protein binding]]
		+	[[Category: Xpg protein]]

OCA at 10:39, 23 December 2015

OCA — Wed, 23 Dec 2015 10:39:11 GMT

←Older revision		Revision as of 10:39, 23 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ekg is ON HOLD	+	The entry 5ekg is ON HOLD until Paper Publication

	Authors: Barros, A.C., Takeda, A.A.S., Fontes, M.R.M.		Authors: Barros, A.C., Takeda, A.A.S., Fontes, M.R.M.

OCA: Protected "5ekg" [edit=sysop:move=sysop]

OCA — Tue, 01 Dec 2015 02:58:45 GMT

Protected "5ekg" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:58, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5ekg is ON HOLD Authors: Barros, A.C., Takeda, A.A.S., Fontes, M.R.M. Description: Crystallization and X-ray Diffraction Data Collection of Importi...

OCA — Tue, 01 Dec 2015 02:58:44 GMT

New page: '''Unreleased structure''' The entry 5ekg is ON HOLD Authors: Barros, A.C., Takeda, A.A.S., Fontes, M.R.M. Description: Crystallization and X-ray Diffraction Data Collection of Importi...

New page

'''Unreleased structure'''

The entry 5ekg is ON HOLD

Authors: Barros, A.C., Takeda, A.A.S., Fontes, M.R.M.

Description: Crystallization and X-ray Diffraction Data Collection of Importin-alpha from Mus musculus Complexed with a XPG NLS Peptide, fragment 2
[[Category: Unreleased Structures]]
[[Category: Barros, A.C]]
[[Category: Takeda, A.A.S]]
[[Category: Fontes, M.R.M]]