3i7l - Revision history

OCA at 07:39, 6 September 2023

OCA — Wed, 06 Sep 2023 07:39:54 GMT

←Older revision		Revision as of 07:39, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3i7l' size='340' side='right'caption='[[3i7l]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3i7l' size='340' side='right'caption='[[3i7l]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i7l]] 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=3I7L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I7L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i7l]] 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=3I7L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I7L 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;'>[[2b5m\|2b5m]], [[3i7h\|3i7h]], [[3i7k\|3i7k]], [[3i7n\|3i7n]], [[3i7o\|3i7o]], [[3i7p\|3i7p]], [[3i89\|3i89]], [[3i8c\|3i8c]], [[3i8e\|3i8e]]</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]] 2.8Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">DDB1, XAP1 ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=9606 HUMAN])~~</td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3i7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7l OCA], [https://pdbe.org/3i7l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i7l RCSB], [https://www.ebi.ac.uk/pdbsum/3i7l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7l 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=3i7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7l OCA], [https://pdbe.org/3i7l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i7l RCSB], [https://www.ebi.ac.uk/pdbsum/3i7l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7l ProSAT]</span></td></tr>
	</table>		</table>
-	== Disease ==
-	[[https://www.uniprot.org/uniprot/DDB2_HUMAN DDB2_HUMAN]] Defects in DDB2 are a cause of xeroderma pigmentosum complementation group E (XP-E) [MIM:[https://omim.org/entry/278740 278740]]; also known as xeroderma pigmentosum V (XP5). XP-E is a rare human autosomal recessive disease characterized by solar sensitivity, high predisposition for developing cancers on areas exposed to sunlight and, in some cases, neurological abnormalities.<ref>PMID:8798680</ref>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DDB1_HUMAN DDB1_HUMAN]] Required for DNA repair. Binds to DDB2 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2.<ref>PMID:12732143</ref> <ref>PMID:15448697</ref> <ref>PMID:14739464</ref> <ref>PMID:15882621</ref> <ref>PMID:16260596</ref> <ref>PMID:16482215</ref> <ref>PMID:17079684</ref> <ref>PMID:16407242</ref> <ref>PMID:16407252</ref> <ref>PMID:16678110</ref> <ref>PMID:16940174</ref> <ref>PMID:17041588</ref> <ref>PMID:16473935</ref> <ref>PMID:18593899</ref> <ref>PMID:18381890</ref> <ref>PMID:18332868</ref> [[https://www.uniprot.org/uniprot/DDB2_HUMAN DDB2_HUMAN]] Required for DNA repair. Binds to DDB1 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as the substrate recognition module for the DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB1-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1). The DDB1-CUL4-ROC1 complex may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. The DDB1-CUL4-ROC1 complex also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. Isoform D1 and isoform D2 inhibit UV-damaged DNA repair.<ref>PMID:14751237</ref> <ref>PMID:9892649</ref> <ref>PMID:10882109</ref> <ref>PMID:11278856</ref> <ref>PMID:11705987</ref> <ref>PMID:12732143</ref> <ref>PMID:12944386</ref> <ref>PMID:15882621</ref> <ref>PMID:16260596</ref> <ref>PMID:16678110</ref> <ref>PMID:16473935</ref> <ref>PMID:18593899</ref>	+	[https://www.uniprot.org/uniprot/DDB1_HUMAN DDB1_HUMAN] Required for DNA repair. Binds to DDB2 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2.<ref>PMID:12732143</ref> <ref>PMID:15448697</ref> <ref>PMID:14739464</ref> <ref>PMID:15882621</ref> <ref>PMID:16260596</ref> <ref>PMID:16482215</ref> <ref>PMID:17079684</ref> <ref>PMID:16407242</ref> <ref>PMID:16407252</ref> <ref>PMID:16678110</ref> <ref>PMID:16940174</ref> <ref>PMID:17041588</ref> <ref>PMID:16473935</ref> <ref>PMID:18593899</ref> <ref>PMID:18381890</ref> <ref>PMID:18332868</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Breugel~~, P C.V~~]]	+	[[Category: Breugel PCV]]
-	[[Category: Li, T]]	+	[[Category: Li T]]
-	[[Category: Robert~~, E I~~]]	+	[[Category: Robert EI]]
-	[[Category: Strubin, M]]	+	[[Category: Strubin M]]
-	[[Category: Zheng, N]]	+	[[Category: Zheng N]]
-	~~[[Category: Alternative splicing]]~~	+
-	~~[[Category: Cytoplasm]]~~	+
-	~~[[Category: Ddb1]]~~	+
-	~~[[Category: Ddb2]]~~	+
-	~~[[Category: Disease mutation]]~~	+
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: H-box motif]]~~	+
-	~~[[Category: Host-virus interaction]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Polymorphism]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Ubl conjugation]]~~	+
-	~~[[Category: Ubl conjugation pathway]]~~	+
-	~~[[Category: Wd repeat]]~~	+
-	~~[[Category: Xeroderma pigmentosum~~]]	+

OCA at 11:00, 13 April 2022

OCA — Wed, 13 Apr 2022 11:00:13 GMT

←Older revision		Revision as of 11:00, 13 April 2022
Line 1:		Line 1:

	==Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2==		==Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2==
-	<StructureSection load='3i7l' size='340' side='right' caption='[[3i7l]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='3i7l' size='340' side='right'caption='[[3i7l]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i7l]] 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=3I7L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3I7L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i7l]] 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=3I7L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I7L FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b5m\|2b5m]], [[3i7h\|3i7h]], [[3i7k\|3i7k]], [[3i7n\|3i7n]], [[3i7o\|3i7o]], [[3i7p\|3i7p]], [[3i89\|3i89]], [[3i8c\|3i8c]], [[3i8e\|3i8e]]</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;'>[[2b5m\|2b5m]], [[3i7h\|3i7h]], [[3i7k\|3i7k]], [[3i7n\|3i7n]], [[3i7o\|3i7o]], [[3i7p\|3i7p]], [[3i89\|3i89]], [[3i8c\|3i8c]], [[3i8e\|3i8e]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDB1, XAP1 ([~~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">DDB1, XAP1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3i7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7l OCA], [~~http~~://pdbe.org/3i7l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3i7l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3i7l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7l 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=3i7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7l OCA], [https://pdbe.org/3i7l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i7l RCSB], [https://www.ebi.ac.uk/pdbsum/3i7l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7l ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/DDB2_HUMAN DDB2_HUMAN]] Defects in DDB2 are a cause of xeroderma pigmentosum complementation group E (XP-E) [MIM:[~~http~~://omim.org/entry/278740 278740]]; also known as xeroderma pigmentosum V (XP5). XP-E is a rare human autosomal recessive disease characterized by solar sensitivity, high predisposition for developing cancers on areas exposed to sunlight and, in some cases, neurological abnormalities.<ref>PMID:8798680</ref>	+	[[https://www.uniprot.org/uniprot/DDB2_HUMAN DDB2_HUMAN]] Defects in DDB2 are a cause of xeroderma pigmentosum complementation group E (XP-E) [MIM:[https://omim.org/entry/278740 278740]]; also known as xeroderma pigmentosum V (XP5). XP-E is a rare human autosomal recessive disease characterized by solar sensitivity, high predisposition for developing cancers on areas exposed to sunlight and, in some cases, neurological abnormalities.<ref>PMID:8798680</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DDB1_HUMAN DDB1_HUMAN]] Required for DNA repair. Binds to DDB2 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2.<ref>PMID:12732143</ref> <ref>PMID:15448697</ref> <ref>PMID:14739464</ref> <ref>PMID:15882621</ref> <ref>PMID:16260596</ref> <ref>PMID:16482215</ref> <ref>PMID:17079684</ref> <ref>PMID:16407242</ref> <ref>PMID:16407252</ref> <ref>PMID:16678110</ref> <ref>PMID:16940174</ref> <ref>PMID:17041588</ref> <ref>PMID:16473935</ref> <ref>PMID:18593899</ref> <ref>PMID:18381890</ref> <ref>PMID:18332868</ref> [[~~http~~://www.uniprot.org/uniprot/DDB2_HUMAN DDB2_HUMAN]] Required for DNA repair. Binds to DDB1 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as the substrate recognition module for the DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB1-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1). The DDB1-CUL4-ROC1 complex may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. The DDB1-CUL4-ROC1 complex also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. Isoform D1 and isoform D2 inhibit UV-damaged DNA repair.<ref>PMID:14751237</ref> <ref>PMID:9892649</ref> <ref>PMID:10882109</ref> <ref>PMID:11278856</ref> <ref>PMID:11705987</ref> <ref>PMID:12732143</ref> <ref>PMID:12944386</ref> <ref>PMID:15882621</ref> <ref>PMID:16260596</ref> <ref>PMID:16678110</ref> <ref>PMID:16473935</ref> <ref>PMID:18593899</ref>	+	[[https://www.uniprot.org/uniprot/DDB1_HUMAN DDB1_HUMAN]] Required for DNA repair. Binds to DDB2 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2.<ref>PMID:12732143</ref> <ref>PMID:15448697</ref> <ref>PMID:14739464</ref> <ref>PMID:15882621</ref> <ref>PMID:16260596</ref> <ref>PMID:16482215</ref> <ref>PMID:17079684</ref> <ref>PMID:16407242</ref> <ref>PMID:16407252</ref> <ref>PMID:16678110</ref> <ref>PMID:16940174</ref> <ref>PMID:17041588</ref> <ref>PMID:16473935</ref> <ref>PMID:18593899</ref> <ref>PMID:18381890</ref> <ref>PMID:18332868</ref> [[https://www.uniprot.org/uniprot/DDB2_HUMAN DDB2_HUMAN]] Required for DNA repair. Binds to DDB1 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as the substrate recognition module for the DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB1-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1). The DDB1-CUL4-ROC1 complex may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. The DDB1-CUL4-ROC1 complex also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. Isoform D1 and isoform D2 inhibit UV-damaged DNA repair.<ref>PMID:14751237</ref> <ref>PMID:9892649</ref> <ref>PMID:10882109</ref> <ref>PMID:11278856</ref> <ref>PMID:11705987</ref> <ref>PMID:12732143</ref> <ref>PMID:12944386</ref> <ref>PMID:15882621</ref> <ref>PMID:16260596</ref> <ref>PMID:16678110</ref> <ref>PMID:16473935</ref> <ref>PMID:18593899</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Breugel, P C.V]]		[[Category: Breugel, P C.V]]
	[[Category: Li, T]]		[[Category: Li, T]]

OCA at 09:52, 19 December 2018

OCA — Wed, 19 Dec 2018 09:52:31 GMT

←Older revision		Revision as of 09:52, 19 December 2018
Line 1:		Line 1:
		+
	==Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2==		==Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2==
	<StructureSection load='3i7l' size='340' side='right' caption='[[3i7l]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3i7l' size='340' side='right' caption='[[3i7l]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b5m\|2b5m]], [[3i7h\|3i7h]], [[3i7k\|3i7k]], [[3i7n\|3i7n]], [[3i7o\|3i7o]], [[3i7p\|3i7p]], [[3i89\|3i89]], [[3i8c\|3i8c]], [[3i8e\|3i8e]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b5m\|2b5m]], [[3i7h\|3i7h]], [[3i7k\|3i7k]], [[3i7n\|3i7n]], [[3i7o\|3i7o]], [[3i7p\|3i7p]], [[3i89\|3i89]], [[3i8c\|3i8c]], [[3i8e\|3i8e]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDB1, XAP1 ([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">DDB1, XAP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3i7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7l OCA], [http://pdbe.org/3i7l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i7l RCSB], [http://www.ebi.ac.uk/pdbsum/3i7l 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=3i7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7l OCA], [http://pdbe.org/3i7l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i7l RCSB], [http://www.ebi.ac.uk/pdbsum/3i7l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7l ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i7/3i7l_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i7/3i7l_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>
Line 43:		Line 44:
	[[Category: Strubin, M]]		[[Category: Strubin, M]]
	[[Category: Zheng, N]]		[[Category: Zheng, N]]
		+	[[Category: Alternative splicing]]
		+	[[Category: Cytoplasm]]
	[[Category: Ddb1]]		[[Category: Ddb1]]
	[[Category: Ddb2]]		[[Category: Ddb2]]
Line 53:		Line 56:
	[[Category: Nucleus]]		[[Category: Nucleus]]
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
		+	[[Category: Polymorphism]]
	[[Category: Protein binding]]		[[Category: Protein binding]]
		+	[[Category: Ubl conjugation]]
	[[Category: Ubl conjugation pathway]]		[[Category: Ubl conjugation pathway]]
	[[Category: Wd repeat]]		[[Category: Wd repeat]]
	[[Category: Xeroderma pigmentosum]]		[[Category: Xeroderma pigmentosum]]

OCA at 08:03, 8 February 2016

OCA — Mon, 08 Feb 2016 08:03:31 GMT

←Older revision		Revision as of 08:03, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3i7l' size='340' side='right' caption='[[3i7l]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3i7l' size='340' side='right' caption='[[3i7l]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i7l]] 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=3I7L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I7L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i7l]] 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=3I7L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I7L FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b5m\|2b5m]], [[3i7h\|3i7h]], [[3i7k\|3i7k]], [[3i7n\|3i7n]], [[3i7o\|3i7o]], [[3i7p\|3i7p]], [[3i89\|3i89]], [[3i8c\|3i8c]], [[3i8e\|3i8e]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b5m\|2b5m]], [[3i7h\|3i7h]], [[3i7k\|3i7k]], [[3i7n\|3i7n]], [[3i7o\|3i7o]], [[3i7p\|3i7p]], [[3i89\|3i89]], [[3i8c\|3i8c]], [[3i8e\|3i8e]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDB1, XAP1 ([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">DDB1, XAP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3i7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i7l RCSB], [http://www.ebi.ac.uk/pdbsum/3i7l 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=3i7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7l OCA], [http://pdbe.org/3i7l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i7l RCSB], [http://www.ebi.ac.uk/pdbsum/3i7l PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 19:		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=3i7l ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3i7l" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Breugel, P C.V]]		[[Category: Breugel, P C.V]]
	[[Category: Li, T]]		[[Category: Li, T]]

OCA at 17:46, 18 December 2014

OCA — Thu, 18 Dec 2014 17:46:25 GMT

←Older revision		Revision as of 17:46, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3i7l~~\| ~~PDB~~=3i7l \| ~~SCENE~~= }}	+	==Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2==
-	===~~Crystal Structure~~ of DDB1 in ~~Complex~~ with the H-~~Box Motif~~ of ~~DDB2~~===	+	<StructureSection load='3i7l' size='340' side='right' caption='[[3i7l]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19966799}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3i7l]] 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=3I7L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I7L FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b5m\|2b5m]], [[3i7h\|3i7h]], [[3i7k\|3i7k]], [[3i7n\|3i7n]], [[3i7o\|3i7o]], [[3i7p\|3i7p]], [[3i89\|3i89]], [[3i8c\|3i8c]], [[3i8e\|3i8e]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDB1, XAP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3i7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i7l RCSB], [http://www.ebi.ac.uk/pdbsum/3i7l PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/DDB2_HUMAN DDB2_HUMAN]] Defects in DDB2 are a cause of xeroderma pigmentosum complementation group E (XP-E) [MIM:[http://omim.org/entry/278740 278740]]; also known as xeroderma pigmentosum V (XP5). XP-E is a rare human autosomal recessive disease characterized by solar sensitivity, high predisposition for developing cancers on areas exposed to sunlight and, in some cases, neurological abnormalities.<ref>PMID:8798680</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DDB1_HUMAN DDB1_HUMAN]] Required for DNA repair. Binds to DDB2 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2.<ref>PMID:12732143</ref> <ref>PMID:15448697</ref> <ref>PMID:14739464</ref> <ref>PMID:15882621</ref> <ref>PMID:16260596</ref> <ref>PMID:16482215</ref> <ref>PMID:17079684</ref> <ref>PMID:16407242</ref> <ref>PMID:16407252</ref> <ref>PMID:16678110</ref> <ref>PMID:16940174</ref> <ref>PMID:17041588</ref> <ref>PMID:16473935</ref> <ref>PMID:18593899</ref> <ref>PMID:18381890</ref> <ref>PMID:18332868</ref> [[http://www.uniprot.org/uniprot/DDB2_HUMAN DDB2_HUMAN]] Required for DNA repair. Binds to DDB1 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as the substrate recognition module for the DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB1-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1). The DDB1-CUL4-ROC1 complex may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. The DDB1-CUL4-ROC1 complex also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. Isoform D1 and isoform D2 inhibit UV-damaged DNA repair.<ref>PMID:14751237</ref> <ref>PMID:9892649</ref> <ref>PMID:10882109</ref> <ref>PMID:11278856</ref> <ref>PMID:11705987</ref> <ref>PMID:12732143</ref> <ref>PMID:12944386</ref> <ref>PMID:15882621</ref> <ref>PMID:16260596</ref> <ref>PMID:16678110</ref> <ref>PMID:16473935</ref> <ref>PMID:18593899</ref>
		+	== 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/i7/3i7l_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 ==
		+	The cullin 4-DNA-damage-binding protein 1 (CUL4-DDB1) ubiquitin ligase machinery regulates diverse cellular functions and can be subverted by pathogenic viruses. Here we report the crystal structure of DDB1 in complex with a central fragment of hepatitis B virus X protein (HBx), whose DDB1-binding activity is important for viral infection. The structure reveals that HBx binds DDB1 through an alpha-helical motif, which is also found in the unrelated paramyxovirus SV5-V protein despite their sequence divergence. Our structure-based functional analysis suggests that, like SV5-V, HBx captures DDB1 to redirect the ubiquitin ligase activity of the CUL4-DDB1 E3 ligase. We also identify the alpha-helical motif shared by these viral proteins in the cellular substrate-recruiting subunits of the E3 complex, the DDB1-CUL4-associated factors (DCAFs) that are functionally mimicked by the viral hijackers. Together, our studies reveal a common yet promiscuous structural element that is important for the assembly of cellular and virally hijacked CUL4-DDB1 E3 complexes.

-	~~==Disease==~~	+	A promiscuous alpha-helical motif anchors viral hijackers and substrate receptors to the CUL4-DDB1 ubiquitin ligase machinery.,Li T, Robert EI, van Breugel PC, Strubin M, Zheng N Nat Struct Mol Biol. 2010 Jan;17(1):105-11. Epub 2009 Dec 6. PMID:19966799<ref>PMID:19966799</ref>
-	~~[[http://www.uniprot.org/uniprot/DDB2_HUMAN DDB2_HUMAN]] Defects in DDB2 are a cause of xeroderma pigmentosum complementation group E (XP~~-~~E) [MIM:[http://omim~~.~~org/entry/278740 278740]]~~; ~~also known as xeroderma pigmentosum V~~ (~~XP5~~)~~. XP~~-~~E is a rare human autosomal recessive disease characterized by solar sensitivity, high predisposition for developing cancers on areas exposed to sunlight and, in some cases, neurological abnormalities~~.<ref>PMID:~~8798680~~</ref>	+

-	~~==Function==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[http:~~//www.uniprot.org/uniprot/DDB1_HUMAN DDB1_HUMAN]] Required for DNA repair. Binds to DDB2 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), ~~6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as~~ a ~~component~~ of ~~numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate~~ the ~~ubiquitination and subsequent proteasomal degradation of target proteins~~. ~~The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1~~. ~~DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at sites~~ of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2.<~~ref~~>PMID:12732143</ref><ref>PMID:15448697</ref><ref>PMID:14739464</ref><ref>PMID:15882621</ref><ref>PMID:16260596</ref><ref>PMID:16482215</ref><ref>PMID:17079684</ref><ref>PMID:16407242</ref><ref>PMID:16407252</ref><ref>PMID:16678110</ref><ref>PMID:16940174</ref><ref>PMID:17041588</ref><ref>PMID:16473935</ref><ref>PMID:18593899</ref><ref>PMID:18381890</ref><ref>PMID:18332868</ref> [[http://www.uniprot.org/uniprot/DDB2_HUMAN DDB2_HUMAN]] Required for DNA repair. Binds to DDB1 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as the substrate recognition module for the DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB1-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1). The DDB1-CUL4-ROC1 complex may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. The DDB1-CUL4-ROC1 complex also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. Isoform D1 and isoform D2 inhibit UV-damaged DNA repair.<ref>PMID:14751237</ref><ref>PMID:9892649</ref><ref>PMID:10882109</ref><ref>PMID:11278856</ref><ref>PMID:11705987</ref><ref>PMID:12732143</ref><ref>PMID:12944386</ref><ref>PMID:15882621</ref><ref>PMID:16260596</ref><ref>PMID:16678110</ref><ref>PMID:16473935</ref><ref>PMID:18593899</~~ref~~>	+	</div>

-	==~~About this Structure~~==	+	==See Also==
-	[[~~3i7l~~]] 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=3I7L OCA].	+	*[[DNA damage-binding protein\|DNA damage-binding protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:019966799</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Breugel, P C.V.]]	+	[[Category: Breugel, P C.V]]
-	[[Category: Li, T.]]	+	[[Category: Li, T]]
-	[[Category: Robert, E I.]]	+	[[Category: Robert, E I]]
-	[[Category: Strubin, M.]]	+	[[Category: Strubin, M]]
-	[[Category: Zheng, N.]]	+	[[Category: Zheng, N]]
	[[Category: Ddb1]]		[[Category: Ddb1]]
	[[Category: Ddb2]]		[[Category: Ddb2]]

OCA at 06:58, 25 March 2013

OCA — Mon, 25 Mar 2013 06:58:58 GMT

←Older revision		Revision as of 06:58, 25 March 2013
Line 2:		Line 2:
	===Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2===		===Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2===
	{{ABSTRACT_PUBMED_19966799}}		{{ABSTRACT_PUBMED_19966799}}
		+
		+	==Disease==
		+	[[http://www.uniprot.org/uniprot/DDB2_HUMAN DDB2_HUMAN]] Defects in DDB2 are a cause of xeroderma pigmentosum complementation group E (XP-E) [MIM:[http://omim.org/entry/278740 278740]]; also known as xeroderma pigmentosum V (XP5). XP-E is a rare human autosomal recessive disease characterized by solar sensitivity, high predisposition for developing cancers on areas exposed to sunlight and, in some cases, neurological abnormalities.<ref>PMID:8798680</ref>
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/DDB1_HUMAN DDB1_HUMAN]] Required for DNA repair. Binds to DDB2 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2.<ref>PMID:12732143</ref><ref>PMID:15448697</ref><ref>PMID:14739464</ref><ref>PMID:15882621</ref><ref>PMID:16260596</ref><ref>PMID:16482215</ref><ref>PMID:17079684</ref><ref>PMID:16407242</ref><ref>PMID:16407252</ref><ref>PMID:16678110</ref><ref>PMID:16940174</ref><ref>PMID:17041588</ref><ref>PMID:16473935</ref><ref>PMID:18593899</ref><ref>PMID:18381890</ref><ref>PMID:18332868</ref> [[http://www.uniprot.org/uniprot/DDB2_HUMAN DDB2_HUMAN]] Required for DNA repair. Binds to DDB1 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as the substrate recognition module for the DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB1-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1). The DDB1-CUL4-ROC1 complex may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. The DDB1-CUL4-ROC1 complex also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. Isoform D1 and isoform D2 inhibit UV-damaged DNA repair.<ref>PMID:14751237</ref><ref>PMID:9892649</ref><ref>PMID:10882109</ref><ref>PMID:11278856</ref><ref>PMID:11705987</ref><ref>PMID:12732143</ref><ref>PMID:12944386</ref><ref>PMID:15882621</ref><ref>PMID:16260596</ref><ref>PMID:16678110</ref><ref>PMID:16473935</ref><ref>PMID:18593899</ref>

	==About this Structure==		==About this Structure==
Line 7:		Line 13:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:019966799</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019966799</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Breugel, P C.V.]]		[[Category: Breugel, P C.V.]]

OCA: Protected "3i7l" [edit=sysop:move=sysop]

OCA — Wed, 13 Mar 2013 10:46:45 GMT

Protected "3i7l" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:46, 13 March 2013

OCA at 10:46, 13 March 2013

OCA — Wed, 13 Mar 2013 10:46:41 GMT

←Older revision		Revision as of 10:46, 13 March 2013
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-	{{Seed}}
-	[[Image:3i7l.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3i7l", 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_3i7l\| PDB=3i7l \| SCENE= }}		{{STRUCTURE_3i7l\| PDB=3i7l \| SCENE= }}
-
	===Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2===		===Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19966799}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19966799 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19966799}}		{{ABSTRACT_PUBMED_19966799}}

	==About this Structure==		==About this Structure==
-	~~3I7L~~ is a 2 ~~chains~~ structure with ~~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=3I7L OCA].	+	[[3i7l]] 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=3I7L OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19966799~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019966799</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Breugel, P C.V.]]		[[Category: Breugel, P C.V.]]
Line 30:		Line 14:
	[[Category: Strubin, M.]]		[[Category: Strubin, M.]]
	[[Category: Zheng, N.]]		[[Category: Zheng, N.]]
-	[[Category: Alternative splicing]]
-	[[Category: Cytoplasm]]
	[[Category: Ddb1]]		[[Category: Ddb1]]
	[[Category: Ddb2]]		[[Category: Ddb2]]
Line 42:		Line 24:
	[[Category: Nucleus]]		[[Category: Nucleus]]
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
-	[[Category: ~~Polymorphism]]~~	+	[[Category: Protein binding]]
-	~~[[Category: Ubl conjugation~~]]	+
	[[Category: Ubl conjugation pathway]]		[[Category: Ubl conjugation pathway]]
	[[Category: Wd repeat]]		[[Category: Wd repeat]]
	[[Category: Xeroderma pigmentosum]]		[[Category: Xeroderma pigmentosum]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 27 19:38:43 2010''

OCA at 17:38, 27 January 2010

OCA — Wed, 27 Jan 2010 17:38:44 GMT

←Older revision		Revision as of 17:38, 27 January 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3i7l.~~jpg~~\|left\|200px]]	+	[[Image:3i7l.png\|left\|200px]]

	<!--		<!--
Line 12:		Line 12:
	===Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2===		===Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19966799}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19966799 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19966799}}

	==About this Structure==		==About this Structure==
-	3I7L 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=3I7L OCA].	+	3I7L is a 2 chains structure with 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=3I7L OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19966799</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Breugel, P C.V.]]		[[Category: Breugel, P C.V.]]
Line 34:		Line 43:
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
	[[Category: Polymorphism]]		[[Category: Polymorphism]]
-	[[Category: Protein binding/protein binding complex]]
	[[Category: Ubl conjugation]]		[[Category: Ubl conjugation]]
	[[Category: Ubl conjugation pathway]]		[[Category: Ubl conjugation pathway]]
Line 40:		Line 48:
	[[Category: Xeroderma pigmentosum]]		[[Category: Xeroderma pigmentosum]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Dec 9 15~~:58:~~30 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 27 19:38:43 2010''

OCA at 13:58, 9 December 2009

OCA — Wed, 09 Dec 2009 13:58:31 GMT

←Older revision		Revision as of 13:58, 9 December 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3i7l.jpg\|left\|200px]]

-	The ~~entry 3i7l~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3i7l", 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_3i7l\| PDB=3i7l \| SCENE= }}

-	~~Authors: Li, T., Robert, E.I., Breugel, P.C.V., Strubin, M., Zheng, N.~~	+	===Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2===

-	Description: Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 22 20~~:34:59 2009''	+	==About this Structure==
		+	3I7L 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=3I7L OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Breugel, P C.V.]]
		+	[[Category: Li, T.]]
		+	[[Category: Robert, E I.]]
		+	[[Category: Strubin, M.]]
		+	[[Category: Zheng, N.]]
		+	[[Category: Alternative splicing]]
		+	[[Category: Cytoplasm]]
		+	[[Category: Ddb1]]
		+	[[Category: Ddb2]]
		+	[[Category: Disease mutation]]
		+	[[Category: Dna damage]]
		+	[[Category: Dna repair]]
		+	[[Category: Dna-binding]]
		+	[[Category: H-box motif]]
		+	[[Category: Host-virus interaction]]
		+	[[Category: Nucleus]]
		+	[[Category: Phosphoprotein]]
		+	[[Category: Polymorphism]]
		+	[[Category: Protein binding/protein binding complex]]
		+	[[Category: Ubl conjugation]]
		+	[[Category: Ubl conjugation pathway]]
		+	[[Category: Wd repeat]]
		+	[[Category: Xeroderma pigmentosum]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 9 15:58:30 2009''