OCA at 15:46, 29 November 2023

OCA — Wed, 29 Nov 2023 15:46:52 GMT

←Older revision		Revision as of 15:46, 29 November 2023
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-	====	+	==Crystal structure of chimeric mutant of GH5 in complex with Z-DNA==
-	<StructureSection load='7c0j' size='340' side='right'caption='[[7c0j]]' scene=''>	+	<StructureSection load='7c0j' size='340' side='right'caption='[[7c0j]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7c0j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus], [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=7C0J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C0J FirstGlance]. <br>
-	</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=7c0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c0j OCA], [~~http~~://pdbe.org/7c0j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7c0j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7c0j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7c0j ProSAT]</span></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]] 2.75Å</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=7c0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c0j OCA], [https://pdbe.org/7c0j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c0j RCSB], [https://www.ebi.ac.uk/pdbsum/7c0j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c0j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[https://www.uniprot.org/uniprot/DSRAD_HUMAN DSRAD_HUMAN] Defects in ADAR are a cause of dyschromatosis symmetrical hereditaria (DSH) [MIM:[https://omim.org/entry/127400 127400]; also known as reticulate acropigmentation of Dohi. DSH is a pigmentary genodermatosis of autosomal dominant inheritance characterized by a mixture of hyperpigmented and hypopigmented macules distributed on the dorsal parts of the hands and feet.<ref>PMID:12916015</ref> <ref>PMID:15146470</ref> <ref>PMID:15659327</ref>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DSRAD_HUMAN DSRAD_HUMAN] Catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA) referred to as A-to-I RNA editing. This may affect gene expression and function in a number of ways that include mRNA translation by changing codons and hence the amino acid sequence of proteins; pre-mRNA splicing by altering splice site recognition sequences; RNA stability by changing sequences involved in nuclease recognition; genetic stability in the case of RNA virus genomes by changing sequences during viral RNA replication; and RNA structure-dependent activities such as microRNA production or targeting or protein-RNA interactions. Can edit both viral and cellular RNAs and can edit RNAs at multiple sites (hyper-editing) or at specific sites (site-specific editing). Its cellular RNA substrates include: bladder cancer-associated protein (BLCAP), neurotransmitter receptors for glutamate (GRIA2) and serotonin (HTR2C) and GABA receptor (GABRA3). Site-specific RNA editing of transcripts encoding these proteins results in amino acid substitutions which consequently alters their functional activities. Exhibits low-level editing at the GRIA2 Q/R site, but edits efficiently at the R/G site and HOTSPOT1. Its viral RNA substrates include: hepatitis C virus (HCV), vesicular stomatitis virus (VSV), measles virus (MV), hepatitis delta virus (HDV), and human immunodeficiency virus type 1 (HIV-1). Exhibits either a proviral (HDV, MV, VSV and HIV-1) or an antiviral effect (HCV) and this can be editing-dependent (HDV and HCV), editing-independent (VSV and MV) or both (HIV-1). Impairs HCV replication via RNA editing at multiple sites. Enhances the replication of MV, VSV and HIV-1 through an editing-independent mechanism via suppression of EIF2AK2/PKR activation and function. Stimulates both the release and infectivity of HIV-1 viral particles by an editing-dependent mechanism where it associates with viral RNAs and edits adenosines in the 5'UTR and the Rev and Tat coding sequence. Can enhance viral replication of HDV via A-to-I editing at a site designated as amber/W, thereby changing an UAG amber stop codon to an UIG tryptophan (W) codon that permits synthesis of the large delta antigen (L-HDAg) which has a key role in the assembly of viral particles. However, high levels of ADAR1 inhibit HDV replication.<ref>PMID:15556947</ref> <ref>PMID:15858013</ref> <ref>PMID:16475990</ref> <ref>PMID:17079286</ref> <ref>PMID:19710021</ref> <ref>PMID:19605474</ref> <ref>PMID:19651874</ref> <ref>PMID:19908260</ref> <ref>PMID:21289159</ref> <ref>PMID:22278222</ref> [https://www.uniprot.org/uniprot/H5_CHICK H5_CHICK] Histone H5 performs the same function as H1, being necessary for the condensation of nucleosome chains into higher order structures, and replaces histone H1 in certain cells.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Left-handed Z-DNA is radically different from the most common right-handed B-DNA and can be stabilized by interactions with the Zalpha domain, which is found in a group of proteins, such as human ADAR1 and viral E3L proteins. It is well-known that most Zalpha domains bind to Z-DNA in a conformation-specific manner and induce rapid B-Z transition in physiological conditions. Although many structural and biochemical studies have identified the detailed interactions between the Zalpha domain and Z-DNA, little is known about the molecular basis of the B-Z transition process. In this study, we successfully converted the B-Z transition-defective Zalpha domain, vvZalphaE3L, into a B-Z converter by improving B-DNA binding ability, suggesting that B-DNA binding is involved in the B-Z transition. In addition, we engineered the canonical B-DNA binding protein GH5 into a Zalpha-like protein having both Z-DNA binding and B-Z transition activities by introducing Z-DNA interacting residues. Crystal structures of these mutants of vvZalphaE3L and GH5 complexed with Z-DNA confirmed the significance of conserved Z-DNA binding interactions. Altogether, our results provide molecular insight into how Zalpha domains obtain unusual conformational specificity and induce the B-Z transition.
		+
		+	Dual conformational recognition by Z-DNA binding protein is important for the B-Z transition process.,Park C, Zheng X, Park CY, Kim J, Lee SK, Won H, Choi J, Kim YG, Choi HJ Nucleic Acids Res. 2020 Dec 16;48(22):12957-12971. doi: 10.1093/nar/gkaa1115. PMID:33245772<ref>PMID:33245772</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7c0j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Adenosine deaminase 3D structures\|Adenosine deaminase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Gallus gallus]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Synthetic construct]]
		+	[[Category: Choi HJ]]
		+	[[Category: Park CH]]

OCA at 12:34, 16 December 2020

OCA — Wed, 16 Dec 2020 12:34:43 GMT

←Older revision		Revision as of 12:34, 16 December 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7c0j ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7c0j' size='340' side='right'caption='[[7c0j]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</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=7c0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c0j OCA], [http://pdbe.org/7c0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7c0j RCSB], [http://www.ebi.ac.uk/pdbsum/7c0j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7c0j ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:10, 27 May 2020

OCA — Wed, 27 May 2020 05:10:48 GMT

←Older revision		Revision as of 05:10, 27 May 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7c0j is ON HOLD	+	The entry 7c0j is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7c0j" [edit=sysop:move=sysop]

OCA — Wed, 06 May 2020 04:57:11 GMT

Protected "7c0j" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:57, 6 May 2020

OCA: New page: '''Unreleased structure''' The entry 7c0j is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 06 May 2020 04:57:10 GMT

New page: '''Unreleased structure''' The entry 7c0j is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7c0j is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7c0j - Revision history

OCA at 15:46, 29 November 2023

OCA at 12:34, 16 December 2020

OCA at 05:10, 27 May 2020

OCA: Protected "7c0j" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7c0j is ON HOLD Authors: Description: Category: Unreleased Structures