View source for 3dd6


==Crystal structure of Rph, an exoribonuclease from Bacillus anthracis at 1.7 A resolution==
<StructureSection load='3dd6' size='340' side='right'caption='[[3dd6]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3dd6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis_str._Ames Bacillus anthracis str. Ames]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DD6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DD6 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]] 1.702&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=3dd6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dd6 OCA], [https://pdbe.org/3dd6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dd6 RCSB], [https://www.ebi.ac.uk/pdbsum/3dd6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dd6 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNPH_BACAN RNPH_BACAN] Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates (By similarity).
== 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/dd/3dd6_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=3dd6 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Maturation of tRNA precursors into functional tRNA molecules requires trimming of the primary transcript at both the 5' and 3' ends. Cleavage of nucleotides from the 3' stem of tRNA precursors, releasing nucleotide diphosphates, is accomplished in Bacillus by a phosphate-dependent exoribonuclease, Rph. The crystal structure of this enzyme from B. anthracis has been solved by molecular replacement to a resolution of 1.7 A and refined to an R factor of 19.3%. There is one molecule in the asymmetric unit; the crystal packing reveals the assembly of the protein into a hexamer arranged as a trimer of dimers. The structure shows two sulfate ions bound in the active-site pocket, probably mimicking the phosphate substrate and the phosphate of the 3'-terminal nucleotide of the tRNA precursor. Three other bound sulfate ions point to likely RNA-binding sites.

The structure of Rph, an exoribonuclease from Bacillus anthracis, at 1.7 A resolution.,Rawlings AE, Blagova EV, Levdikov VM, Fogg MJ, Wilson KS, Wilkinson AJ Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jan 1;65(Pt 1):2-7., Epub 2008 Dec 25. PMID:19153445<ref>PMID:19153445</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3dd6" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus anthracis str. Ames]]
[[Category: Large Structures]]
[[Category: Blagova EV]]
[[Category: Fogg MJ]]
[[Category: Levdikov VM]]
[[Category: Rawlings AE]]
[[Category: Wilkinson AJ]]
[[Category: Wilson KS]]