This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1qgp

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (23:48, 27 December 2023) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1qgp.jpg|left|200px]]<br /><applet load="1qgp" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1qgp" />
 
-
'''NMR STRUCTURE OF THE Z-ALPHA DOMAIN OF ADAR1, 15 STRUCTURES'''<br />
 
-
==Overview==
+
==NMR STRUCTURE OF THE Z-ALPHA DOMAIN OF ADAR1, 15 STRUCTURES==
-
Double-stranded RNA deaminase I (ADAR1) contains the Z-DNA binding domain, Zalpha. Here we report the solution structure of free Zalpha and map the, interaction surface with Z-DNA, confirming roles previously assigned to, residues by mutagenesis. Comparison with the crystal structure of the, (Zalpha)(2)/Z-DNA complex shows that most Z-DNA contacting residues in, free Zalpha are prepositioned to bind Z-DNA, thus minimizing the entropic, cost of binding. Comparison with homologous, (alpha+beta)helix-turn-helix/B-DNA complexes suggests that binding of, Zalpha to B-DNA is disfavored by steric hindrance, but does not eliminate, the possibility that related domains may bind to both B- and Z-DNA.
+
<StructureSection load='1qgp' size='340' side='right'caption='[[1qgp]]' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1qgp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QGP FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1qgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qgp OCA], [https://pdbe.org/1qgp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qgp RCSB], [https://www.ebi.ac.uk/pdbsum/1qgp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qgp 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/qg/1qgp_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=1qgp ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Double-stranded RNA deaminase I (ADAR1) contains the Z-DNA binding domain Zalpha. Here we report the solution structure of free Zalpha and map the interaction surface with Z-DNA, confirming roles previously assigned to residues by mutagenesis. Comparison with the crystal structure of the (Zalpha)(2)/Z-DNA complex shows that most Z-DNA contacting residues in free Zalpha are prepositioned to bind Z-DNA, thus minimizing the entropic cost of binding. Comparison with homologous (alpha+beta)helix-turn-helix/B-DNA complexes suggests that binding of Zalpha to B-DNA is disfavored by steric hindrance, but does not eliminate the possibility that related domains may bind to both B- and Z-DNA.
-
==Disease==
+
The solution structure of the Zalpha domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA.,Schade M, Turner CJ, Kuhne R, Schmieder P, Lowenhaupt K, Herbert A, Rich A, Oschkinat H Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12465-70. PMID:10535945<ref>PMID:10535945</ref>
-
Known diseases associated with this structure: Dyschromatosis symmetrica hereditaria OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601059 601059]]
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
1QGP 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1QGP OCA].
+
</div>
 +
<div class="pdbe-citations 1qgp" style="background-color:#fffaf0;"></div>
-
==Reference==
+
==See Also==
-
The solution structure of the Zalpha domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA., Schade M, Turner CJ, Kuhne R, Schmieder P, Lowenhaupt K, Herbert A, Rich A, Oschkinat H, Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12465-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10535945 10535945]
+
*[[Adenosine deaminase 3D structures|Adenosine deaminase 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Herbert, A.]]
+
[[Category: Herbert A]]
-
[[Category: Kuehne, R.]]
+
[[Category: Kuehne R]]
-
[[Category: Lowenhaupt, K.]]
+
[[Category: Lowenhaupt K]]
-
[[Category: Oschkinat, H.]]
+
[[Category: Oschkinat H]]
-
[[Category: Rich, A.]]
+
[[Category: Rich A]]
-
[[Category: Schade, M.]]
+
[[Category: Schade M]]
-
[[Category: Schmieder, P.]]
+
[[Category: Schmieder P]]
-
[[Category: Turner, C.J.]]
+
[[Category: Turner CJ]]
-
[[Category: adar1]]
+
-
[[Category: helix- turn-helix]]
+
-
[[Category: rna-editing]]
+
-
[[Category: z-alpha-z-dna binding domain]]
+
-
[[Category: z-dna recognition]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 16:44:33 2008''
+

Current revision

NMR STRUCTURE OF THE Z-ALPHA DOMAIN OF ADAR1, 15 STRUCTURES

PDB ID 1qgp

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1qgp"
Personal tools