5sxh - Revision history

OCA at 12:50, 4 October 2023

OCA — Wed, 04 Oct 2023 12:50:13 GMT

←Older revision		Revision as of 12:50, 4 October 2023
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	<StructureSection load='5sxh' size='340' side='right'caption='[[5sxh]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='5sxh' size='340' side='right'caption='[[5sxh]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5sxh]] 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=5SXH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5SXH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5sxh]] 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=5SXH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SXH FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.78Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~APOBEC3B ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5sxh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sxh OCA], [~~http~~://pdbe.org/5sxh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5sxh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5sxh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5sxh 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=5sxh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sxh OCA], [https://pdbe.org/5sxh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sxh RCSB], [https://www.ebi.ac.uk/pdbsum/5sxh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sxh ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ABC3B_HUMAN ABC3B_HUMAN]] DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single-or double-stranded RNA. Exhibits antiviral activity against simian immunodeficiency virus (SIV), hepatitis B virus (HBV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons.<ref>PMID:12859895</ref> <ref>PMID:15466872</ref> <ref>PMID:16060832</ref> <ref>PMID:16527742</ref> <ref>PMID:20062055</ref> <ref>PMID:22457529</ref>	+	[https://www.uniprot.org/uniprot/ABC3B_HUMAN ABC3B_HUMAN] DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single-or double-stranded RNA. Exhibits antiviral activity against simian immunodeficiency virus (SIV), hepatitis B virus (HBV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons.<ref>PMID:12859895</ref> <ref>PMID:15466872</ref> <ref>PMID:16060832</ref> <ref>PMID:16527742</ref> <ref>PMID:20062055</ref> <ref>PMID:22457529</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aihara, H]]	+	[[Category: Aihara H]]
-	[[Category: Kurahashi, K]]	+	[[Category: Kurahashi K]]
-	[[Category: Shi, K]]	+	[[Category: Shi K]]
-	~~[[Category: Deaminase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 12:25, 25 December 2019

OCA — Wed, 25 Dec 2019 12:25:15 GMT

←Older revision		Revision as of 12:25, 25 December 2019
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	==Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B==		==Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B==
-	<StructureSection load='5sxh' size='340' side='right' caption='[[5sxh]], [[Resolution\|resolution]] 1.78Å' scene=''>	+	<StructureSection load='5sxh' size='340' side='right'caption='[[5sxh]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5sxh]] 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=5SXH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SXH FirstGlance]. <br>		<table><tr><td colspan='2'>[[5sxh]] 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=5SXH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SXH FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Aihara, H]]		[[Category: Aihara, H]]
	[[Category: Kurahashi, K]]		[[Category: Kurahashi, K]]

OCA at 06:30, 18 April 2018

OCA — Wed, 18 Apr 2018 06:30:21 GMT

←Older revision		Revision as of 06:30, 18 April 2018
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	<StructureSection load='5sxh' size='340' side='right' caption='[[5sxh]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='5sxh' size='340' side='right' caption='[[5sxh]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5sxh]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SXH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SXH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5sxh]] 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=5SXH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SXH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APOBEC3B ([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=5sxh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sxh OCA], [http://pdbe.org/5sxh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5sxh RCSB], [http://www.ebi.ac.uk/pdbsum/5sxh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5sxh ProSAT]</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=5sxh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sxh OCA], [http://pdbe.org/5sxh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5sxh RCSB], [http://www.ebi.ac.uk/pdbsum/5sxh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5sxh ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Aihara, H]]		[[Category: Aihara, H]]
	[[Category: Kurahashi, K]]		[[Category: Kurahashi, K]]

OCA at 08:26, 27 December 2017

OCA — Wed, 27 Dec 2017 08:26:22 GMT

←Older revision		Revision as of 08:26, 27 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5sxh is ~~ON HOLD~~	+	==Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B==
		+	<StructureSection load='5sxh' size='340' side='right' caption='[[5sxh]], [[Resolution\|resolution]] 1.78Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5sxh]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SXH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SXH FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5sxh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sxh OCA], [http://pdbe.org/5sxh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5sxh RCSB], [http://www.ebi.ac.uk/pdbsum/5sxh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5sxh ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ABC3B_HUMAN ABC3B_HUMAN]] DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single-or double-stranded RNA. Exhibits antiviral activity against simian immunodeficiency virus (SIV), hepatitis B virus (HBV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons.<ref>PMID:12859895</ref> <ref>PMID:15466872</ref> <ref>PMID:16060832</ref> <ref>PMID:16527742</ref> <ref>PMID:20062055</ref> <ref>PMID:22457529</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The APOBEC3B (A3B) single-stranded DNA (ssDNA) cytosine deaminase has important roles in innate immunity but is also a major endogenous source of mutations in cancer. Previous structural studies showed that the C-terminal catalytic domain of human A3B has a tightly closed active site, and rearrangement of the surrounding loops is required for binding to substrate ssDNA. Here we report structures of the A3B catalytic domain in a new crystal form that show alternative, yet still closed, conformations of active site loops. All-atom molecular dynamics simulations support the dynamic behavior of active site loops and recapitulate the distinct modes of interactions that maintain a closed active site. Replacing segments of A3B loop 1 to mimic the more potent cytoplasmic deaminase APOBEC3A leads to elevated ssDNA deaminase activity, likely by facilitating opening of the active site. These data collectively suggest that conformational equilibrium of the A3B active site loops, skewed toward being closed, controls enzymatic activity by regulating binding to ssDNA substrates.

-	~~Authors~~:	+	Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.,Shi K, Demir O, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro RE, Aihara H Sci Rep. 2017 Dec 12;7(1):17415. doi: 10.1038/s41598-017-17694-3. PMID:29234087<ref>PMID:29234087</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5sxh" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Aihara, H]]
		+	[[Category: Kurahashi, K]]
		+	[[Category: Shi, K]]
		+	[[Category: Deaminase]]
		+	[[Category: Hydrolase]]

OCA at 05:44, 13 December 2017

OCA — Wed, 13 Dec 2017 05:44:06 GMT

←Older revision		Revision as of 05:44, 13 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5sxh is ON HOLD ~~until Feb 09 2019~~	+	The entry 5sxh is ON HOLD

	Authors:		Authors:

OCA at 13:20, 27 September 2017

OCA — Wed, 27 Sep 2017 13:20:35 GMT

←Older revision		Revision as of 13:20, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5sxh is ON HOLD until ~~Paper Publication~~	+	The entry 5sxh is ON HOLD until Feb 09 2019

	Authors:		Authors:

OCA at 19:29, 5 October 2016

OCA — Wed, 05 Oct 2016 19:29:41 GMT

←Older revision		Revision as of 19:29, 5 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Fri, 09 Sep 2016 15:23:11 GMT

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

←Older revision

Revision as of 15:23, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5sxh is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Fri, 09 Sep 2016 15:23:10 GMT

New page: '''Unreleased structure''' The entry 5sxh is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5sxh is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]