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1vfg

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(New page: 200px<br /><applet load="1vfg" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vfg, resolution 2.8&Aring;" /> '''Crystal structure of ...)
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[[Image:1vfg.gif|left|200px]]<br /><applet load="1vfg" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1vfg, resolution 2.8&Aring;" />
 
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'''Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog'''<br />
 
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==Overview==
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==Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog==
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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.
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<StructureSection load='1vfg' size='340' side='right'caption='[[1vfg]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
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<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>
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<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>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vf/1vfg_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==About this Structure==
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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>
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1VFG 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 APC as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1VFG OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15295603 15295603]
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</div>
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<div class="pdbe-citations 1vfg" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
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[[Category: Polynucleotide adenylyltransferase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Thermotoga maritima]]
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[[Category: Fukai, S.]]
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[[Category: Fukai S]]
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[[Category: Ishitani, R.]]
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[[Category: Ishitani R]]
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[[Category: Nureki, O.]]
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[[Category: Nureki O]]
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[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
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[[Category: Takeuchi N]]
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[[Category: Takeuchi, N.]]
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[[Category: Tomita K]]
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[[Category: Tomita, K.]]
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[[Category: Ueda T]]
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[[Category: Ueda, T.]]
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[[Category: Vassylyev DG]]
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[[Category: Vassylyev, D.G.]]
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[[Category: APC]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: rna]]
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[[Category: rsgi]]
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[[Category: structural genomics]]
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[[Category: transferase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:20:14 2007''
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Current revision

Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog

PDB ID 1vfg

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