2acj: Difference between revisions

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OCA

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-[[Image:2acj.gif|left|200px]]<br />
-<applet load="2acj" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2acj, resolution 2.60&Aring;" />
-'''Crystal structure of the B/Z junction containing DNA bound to Z-DNA binding proteins'''<br />
-==Overview==
+==Crystal structure of the B/Z junction containing DNA bound to Z-DNA binding proteins==
-Left-handed Z-DNA is a higher-energy form of the double helix, stabilized, by negative supercoiling generated by transcription or unwrapping, nucleosomes. Regions near the transcription start site frequently contain, sequence motifs favourable for forming Z-DNA, and formation of Z-DNA near, the promoter region stimulates transcription. Z-DNA is also stabilized by, specific protein binding; several proteins have been identified with low, nanomolar binding constants. Z-DNA occurs in a dynamic state, forming as a, result of physiological processes then relaxing to the right-handed B-DNA., Each time a DNA segment turns into Z-DNA, two B-Z junctions form. These, have been examined extensively, but their structure was unknown. Here we, describe the structure of a B-Z junction as revealed by X-ray, crystallography at 2.6 A resolution. A 15-base-pair segment of DNA is, stabilized at one end in the Z conformation by Z-DNA binding proteins, while the other end remains B-DNA. Continuous stacking of bases between, B-DNA and Z-DNA segments is found, with the breaking of one base pair at, the junction and extrusion of the bases on each side (Fig. 1). These, extruded bases may be sites for DNA modification.
+<StructureSection load='2acj' size='340' side='right'caption='[[2acj]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2acj]] is a 6 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=2ACJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ACJ FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</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=2acj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2acj OCA], [https://pdbe.org/2acj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2acj RCSB], [https://www.ebi.ac.uk/pdbsum/2acj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2acj ProSAT]</span></td></tr>
+</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>
+== 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/ac/2acj_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/main_output.php?pdb_ID=2acj ConSurf].
+<div style="clear:both"></div>
-==Disease==
+==See Also==
-Known diseases associated with this structure: Dyschromatosis symmetrica hereditaria OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601059 601059]]
+*[[Adenosine deaminase 3D structures|Adenosine deaminase 3D structures]]
+*[[Z-DNA|Z-DNA]]
-==About this Structure==
+== References ==
-ACJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2ACJ OCA].
+<references/>
+__TOC__
-==Reference==
+</StructureSection>
-Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases., Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK, Nature. 2005 Oct 20;437(7062):1183-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16237447 16237447]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Ha, S.C.]]
+[[Category: Ha SC]]
-[[Category: Kim, K.K.]]
+[[Category: Kim KK]]
-[[Category: Kim, Y.G.]]
+[[Category: Kim Y-G]]
-[[Category: Lowenhaupt, K.]]
+[[Category: Lowenhaupt K]]
-[[Category: Rich, A.]]
+[[Category: Rich A]]
-[[Category: a b-z juction]]
-[[Category: protein-dna complex]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 20:48:48 2007''