Proteopedia

2dr8: Difference between revisions

← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2dr8.gif|left|200px]]


{{Structure
==Complex structure of CCA-adding enzyme with tRNAminiDC and CTP==
|PDB= 2dr8 |SIZE=350|CAPTION= <scene name='initialview01'>2dr8</scene>, resolution 2.50&Aring;
<StructureSection load='2dr8' size='340' side='right'caption='[[2dr8]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CTP:CYTIDINE-5&#39;-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
<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>
|ACTIVITY=
</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>
|GENE=
<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>
|DOMAIN=
<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>
|RELATEDENTRY=[[2dr5|2DR5]], [[2dr7|2DR7]], [[2dr9|2DR9]], [[2dra|2DRA]], [[2drb|2DRB]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dr8 OCA], [http://www.ebi.ac.uk/pdbsum/2dr8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dr8 RCSB]</span>
== 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>


'''Complex structure of CCA-adding enzyme with tRNAminiDC and CTP'''
==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>
2DR8 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=2DR8 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: 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 Mon Mar 31 02:38:21 2008''

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/w/2dr8"