1vfg: Difference between revisions
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==Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog== | |||
<StructureSection load='1vfg' size='340' side='right'caption='[[1vfg]], [[Resolution|resolution]] 2.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1vfg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] and [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VFG 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]] 2.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</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=1vfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vfg OCA], [https://pdbe.org/1vfg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vfg RCSB], [https://www.ebi.ac.uk/pdbsum/1vfg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vfg ProSAT], [https://www.topsan.org/Proteins/RSGI/1vfg TOPSAN]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/AATNT_AQUAE AATNT_AQUAE] tRNA nucleotidyltransferase involved in the synthesis of the tRNA CCA terminus. Adds the terminal adenosine residue to tRNA (PubMed:11701927, PubMed:25914059). Can incorporate CMP into tRNA ending with C74C75 (tRNACC), with very weak efficiency (PubMed:25914059).<ref>PMID:11701927</ref> <ref>PMID:25914059</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/vf/1vfg_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=1vfg ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The 3'-terminal CCA nucleotide sequence (positions 74-76) of transfer RNA is essential for amino acid attachment and interaction with the ribosome during protein synthesis. The CCA sequence is synthesized de novo and/or repaired by a template-independent RNA polymerase, 'CCA-adding enzyme', using CTP and ATP as substrates. Despite structural and biochemical studies, the mechanism by which the CCA-adding enzyme synthesizes the defined sequence without a nucleic acid template remains elusive. Here we present the crystal structure of Aquifex aeolicus CCA-adding enzyme, bound to a primer tRNA lacking the terminal adenosine and an incoming ATP analogue, at 2.8 A resolution. The enzyme enfolds the acceptor T helix of the tRNA molecule. In the catalytic pocket, C75 is adjacent to ATP, and their base moieties are stacked. The complementary pocket for recognizing C74-C75 of tRNA forms a 'protein template' for the penultimate two nucleotides, mimicking the nucleotide template used by template-dependent polymerases. These results are supported by systematic analyses of mutants. Our structure represents the 'pre-insertion' stage of selecting the incoming nucleotide and provides the structural basis for the mechanism underlying template-independent RNA polymerization. | |||
Structural basis for template-independent RNA polymerization.,Tomita K, Fukai S, Ishitani R, Ueda T, Takeuchi N, Vassylyev DG, Nureki O Nature. 2004 Aug 5;430(7000):700-4. PMID:15295603<ref>PMID:15295603</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1vfg" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
== | __TOC__ | ||
< | </StructureSection> | ||
[[Category: Aquifex aeolicus]] | [[Category: Aquifex aeolicus]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Thermotoga maritima]] | ||
[[Category: | [[Category: Fukai S]] | ||
[[Category: | [[Category: Ishitani R]] | ||
[[Category: | [[Category: Nureki O]] | ||
[[Category: Takeuchi | [[Category: Takeuchi N]] | ||
[[Category: Tomita | [[Category: Tomita K]] | ||
[[Category: Ueda | [[Category: Ueda T]] | ||
[[Category: Vassylyev | [[Category: Vassylyev DG]] | ||
Latest revision as of 00:03, 28 December 2023
Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog
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