2dr8: Difference between revisions

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New page: left|200px<br /><applet load="2dr8" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dr8, resolution 2.50Å" /> '''Complex structure of...
 
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[[Image:2dr8.gif|left|200px]]<br /><applet load="2dr8" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2dr8, resolution 2.50&Aring;" />
'''Complex structure of CCA-adding enzyme with tRNAminiDC and CTP'''<br />


==Overview==
==Complex structure of CCA-adding enzyme with tRNAminiDC and CTP==
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.
<StructureSection load='2dr8' size='340' side='right'caption='[[2dr8]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2dr8]] 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=2DR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DR8 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]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2dr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dr8 OCA], [https://pdbe.org/2dr8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dr8 RCSB], [https://www.ebi.ac.uk/pdbsum/2dr8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dr8 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/2dr8_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=2dr8 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2DR8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus] with SO4, MG and CTP as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DR8 OCA].
*[[CCA-adding enzyme 3D structures|CCA-adding enzyme 3D structures]]
 
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
==Reference==
== References ==
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17051158 17051158]
<references/>
__TOC__
</StructureSection>
[[Category: Archaeoglobus fulgidus]]
[[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: CTP]]
[[Category: MG]]
[[Category: SO4]]
[[Category: protein-rna complex]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:44:19 2007''

Latest revision as of 16:48, 13 March 2024

Complex structure of CCA-adding enzyme with tRNAminiDC and CTPComplex structure of CCA-adding enzyme with tRNAminiDC and CTP

Structural highlights

2dr8 is a 2 chain structure with sequence from Archaeoglobus fulgidus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Okabe M, Tomita K, Ishitani R, Ishii R, Takeuchi N, Arisaka F, Nureki O, Yokoyama S. Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure. EMBO J. 2003 Nov 3;22(21):5918-27. PMID:14592988 doi:http://dx.doi.org/10.1093/emboj/cdg563

2dr8, resolution 2.50Å

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