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New page: left|200px<br /><applet load="1ww1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ww1, resolution 2.60Å" /> '''Crystal structure of...
 
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[[Image:1ww1.gif|left|200px]]<br /><applet load="1ww1" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ww1, resolution 2.60&Aring;" />
'''Crystal structure of tRNase Z from Thermotoga maritima'''<br />


==Overview==
==Crystal structure of tRNase Z from Thermotoga maritima==
The maturation of the tRNA 3' end is catalyzed by a tRNA 3' processing, endoribonuclease named tRNase Z (RNase Z or 3'-tRNase) in eukaryotes, Archaea, and some bacteria. The tRNase Z generally cuts the 3' extra, sequence from the precursor tRNA after the discriminator nucleotide. In, contrast, Thermotoga maritima tRNase Z cleaves the precursor tRNA, precisely after the CCA sequence. In this study, we determined the crystal, structure of T. maritima tRNase Z at 2.6-A resolution. The tRNase Z has a, four-layer alphabeta/betaalpha sandwich fold, which is classified as a, metallo-beta-lactamase fold, and forms a dimer. The active site is located, at one edge of the beta-sandwich and is composed of conserved motifs., Based on the structure, we constructed a docking model with the tRNAs that, suggests how tRNase Z may recognize the substrate tRNAs.
<StructureSection load='1ww1' size='340' side='right'caption='[[1ww1]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1ww1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WW1 FirstGlance]. <br>
1WW1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_Z Ribonuclease Z], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.11 3.1.26.11] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WW1 OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ww1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ww1 OCA], [https://pdbe.org/1ww1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ww1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ww1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ww1 ProSAT], [https://www.topsan.org/Proteins/RSGI/1ww1 TOPSAN]</span></td></tr>
Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima., Ishii R, Minagawa A, Takaku H, Takagi M, Nashimoto M, Yokoyama S, J Biol Chem. 2005 Apr 8;280(14):14138-44. Epub 2005 Jan 27. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15701599 15701599]
</table>
[[Category: Ribonuclease Z]]
== Function ==
[[Category: Single protein]]
[https://www.uniprot.org/uniprot/Q9WZW8_THEMA Q9WZW8_THEMA]  
[[Category: Thermotoga maritima]]
== Evolutionary Conservation ==
[[Category: Ishii, R.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
Check<jmol>
[[Category: Yokoyama, S.]]
  <jmolCheckbox>
[[Category: ZN]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ww/1ww1_consurf.spt"</scriptWhenChecked>
[[Category: metallo-beta-lactamase fold]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: riken structural genomics/proteomics initiative]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: rsgi]]
  </jmolCheckbox>
[[Category: structural genomics]]
</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=1ww1 ConSurf].
 
<div style="clear:both"></div>
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 00:52:28 2007''
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermotoga maritima MSB8]]
[[Category: Ishii R]]
[[Category: Yokoyama S]]

Latest revision as of 13:34, 13 March 2024

Crystal structure of tRNase Z from Thermotoga maritima

1ww1, resolution 2.60Å

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