2dra: Difference between revisions

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-[[Image:2dra.gif|left|200px]]
-<!--
+==Complex structure of CCA-adding enzyme with tRNAminiDCC and ATP==
-The line below this paragraph, containing "STRUCTURE_2dra", creates the "Structure Box" on the page.
+<StructureSection load='2dra' size='340' side='right'caption='[[2dra]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2dra]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DRA FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2dra|  PDB=2dra  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dra OCA], [https://pdbe.org/2dra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dra RCSB], [https://www.ebi.ac.uk/pdbsum/2dra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dra ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CCA_ARCFU CCA_ARCFU] Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate.<ref>PMID:14592988</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/dr/2dra_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=2dra ConSurf].
+<div style="clear:both"></div>
-'''Complex structure of CCA-adding enzyme with tRNAminiDCC and ATP'''
+==See Also==
+*[[CCA-adding enzyme 3D structures|CCA-adding enzyme 3D structures]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-==Overview==
+== References ==
-CCA-adding polymerase matures the essential 3'-CCA terminus of transfer RNA without any nucleic-acid template. However, it remains unclear how the correct nucleotide triphosphate is selected in each reaction step and how the polymerization is driven by the protein and RNA dynamics. Here we present complete sequential snapshots of six complex structures of CCA-adding enzyme and four distinct RNA substrates with and without CTP (cytosine triphosphate) or ATP (adenosine triphosphate). The CCA-lacking RNA stem extends by one base pair to force the discriminator nucleoside into the active-site pocket, and then tracks back after incorporation of the first cytosine monophosphate (CMP). Accommodation of the second CTP clamps the catalytic cleft, inducing a reorientation of the turn, which flips C74 to allow CMP to be accepted. In contrast, after the second CMP is added, the polymerase and RNA primer are locked in the closed state, which directs the subsequent A addition. Between the CTP- and ATP-binding stages, the side-chain conformation of Arg 224 changes markedly; this is controlled by the global motion of the enzyme and position of the primer terminus, and is likely to achieve the CTP/ATP discrimination, depending on the polymerization stage. Throughout the CCA-adding reaction, the enzyme tail domain firmly anchors the TPsiC-loop of the tRNA, which ensures accurate polymerization and termination.
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-DRA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DRA OCA].
-==Reference==
-Complete crystallographic analysis of the dynamics of CCA sequence addition., Tomita K, Ishitani R, Fukai S, Nureki O, Nature. 2006 Oct 26;443(7114):956-60. Epub 2006 Oct 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17051158 17051158]
 [[Category: Archaeoglobus fulgidus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Fukai, S.]]
+[[Category: Fukai S]]
-[[Category: Ishitani, R.]]
+[[Category: Ishitani R]]
-[[Category: Nureki, O.]]
+[[Category: Nureki O]]
-[[Category: Tomita, K.]]
+[[Category: Tomita K]]
-[[Category: Protein-rna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 01:00:14 2008''