1wwr: Difference between revisions

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OCA

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-[[Image:1wwr.gif|left|200px]]<br /><applet load="1wwr" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1wwr, resolution 1.80&Aring;" />
-'''Crystal structure of tRNA adenosine deaminase TadA from Aquifex aeolicus'''<br />
-==Overview==
+==Crystal structure of tRNA adenosine deaminase TadA from Aquifex aeolicus==
-The bacterial tRNA adenosine deaminase (TadA) generates inosine by, deaminating the adenosine residue at the wobble position of tRNA(Arg-2)., This modification is essential for the decoding system. In this study, we, determined the crystal structure of Aquifex aeolicus TadA at a 1.8-A, resolution. This is the first structure of a deaminase acting on tRNA. A., aeolicus TadA has an alpha/beta/alpha three-layered fold and forms a, homodimer. The A. aeolicus TadA dimeric structure is completely different, from the tetrameric structure of yeast CDD1, which deaminates mRNA and, cytidine, but is similar to the dimeric structure of yeast cytosine, deaminase. However, in the A. aeolicus TadA structure, the shapes of the, C-terminal helix and the regions between the beta4 and beta5 strands are, quite distinct from those of yeast cytosine deaminase and a large cavity, is produced. This cavity contains many conserved amino acid residues that, are likely to be involved in either catalysis or tRNA binding. We made a, docking model of TadA with the tRNA anticodon stem loop.
+<StructureSection load='1wwr' size='340' side='right'caption='[[1wwr]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1wwr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WWR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WWR 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]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[https://proteopedia.org/fgij/fg.htm?mol=1wwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wwr OCA], [https://pdbe.org/1wwr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wwr RCSB], [https://www.ebi.ac.uk/pdbsum/1wwr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wwr ProSAT], [https://www.topsan.org/Proteins/RSGI/1wwr TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TADA_AQUAE TADA_AQUAE] Deaminates adenosine-34 to inosine in tRNA-Arg2.
+== 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/ww/1wwr_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=1wwr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The bacterial tRNA adenosine deaminase (TadA) generates inosine by deaminating the adenosine residue at the wobble position of tRNA(Arg-2). This modification is essential for the decoding system. In this study, we determined the crystal structure of Aquifex aeolicus TadA at a 1.8-A resolution. This is the first structure of a deaminase acting on tRNA. A. aeolicus TadA has an alpha/beta/alpha three-layered fold and forms a homodimer. The A. aeolicus TadA dimeric structure is completely different from the tetrameric structure of yeast CDD1, which deaminates mRNA and cytidine, but is similar to the dimeric structure of yeast cytosine deaminase. However, in the A. aeolicus TadA structure, the shapes of the C-terminal helix and the regions between the beta4 and beta5 strands are quite distinct from those of yeast cytosine deaminase and a large cavity is produced. This cavity contains many conserved amino acid residues that are likely to be involved in either catalysis or tRNA binding. We made a docking model of TadA with the tRNA anticodon stem loop.
-==About this Structure==
+Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus.,Kuratani M, Ishii R, Bessho Y, Fukunaga R, Sengoku T, Shirouzu M, Sekine S, Yokoyama S J Biol Chem. 2005 Apr 22;280(16):16002-8. Epub 2005 Jan 26. PMID:15677468<ref>PMID:15677468</ref>
-WWR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WWR OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus., Kuratani M, Ishii R, Bessho Y, Fukunaga R, Sengoku T, Shirouzu M, Sekine S, Yokoyama S, J Biol Chem. 2005 Apr 22;280(16):16002-8. Epub 2005 Jan 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15677468 15677468]
+</div>
+<div class="pdbe-citations 1wwr" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Adenosine deaminase 3D structures|Adenosine deaminase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Aquifex aeolicus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bessho, Y.]]
+[[Category: Bessho Y]]
-[[Category: Fukunaga, R.]]
+[[Category: Fukunaga R]]
-[[Category: Ishii, R.]]
+[[Category: Ishii R]]
-[[Category: Kuratani, M.]]
+[[Category: Kuratani M]]
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+[[Category: Sekine S]]
-[[Category: Sekine, S.]]
+[[Category: Sengoku T]]
-[[Category: Sengoku, T.]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S.]]
-[[Category: ZN]]
-[[Category: homodimer]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rsgi]]
-[[Category: structural genomics]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:43:28 2007''