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1yt3

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[[Image:1yt3.gif|left|200px]]
 
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{{Structure
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==Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing==
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|PDB= 1yt3 |SIZE=350|CAPTION= <scene name='initialview01'>1yt3</scene>, resolution 1.60&Aring;
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<StructureSection load='1yt3' size='340' side='right'caption='[[1yt3]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
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<table><tr><td colspan='2'>[[1yt3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YT3 FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] </span>
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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]] 1.6&#8491;</td></tr>
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|GENE= RND ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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|DOMAIN=
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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=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [https://pdbe.org/1yt3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [https://www.ebi.ac.uk/pdbsum/1yt3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yt3 ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [http://www.ebi.ac.uk/pdbsum/1yt3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/RND_ECOLI RND_ECOLI] Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides.<ref>PMID:3041371</ref> <ref>PMID:6263886</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/yt/1yt3_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=1yt3 ConSurf].
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<div style="clear:both"></div>
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'''Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing'''
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==See Also==
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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== References ==
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==Overview==
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<references/>
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RNase D (RND) is one of seven exoribonucleases identified in Escherichia coli. RNase D has homologs in many eubacteria and eukaryotes, and has been shown to contribute to the 3' maturation of several stable RNAs. Here, we report the 1.6 A resolution crystal structure of E. coli RNase D. The conserved DEDD residues of RNase D fold into an arrangement very similar to the Klenow fragment exonuclease domain. Besides the catalytic domain, RNase D also contains two structurally similar alpha-helical domains with no discernible sequence homology between them. These closely resemble the HRDC domain previously seen in RecQ-family helicases and several other proteins acting on nucleic acids. More interestingly, the DEDD catalytic domain and the two helical domains come together to form a ring-shaped structure. The ring-shaped architecture of E. coli RNase D and the HRDC domains likely play a major role in determining the substrate specificity of this exoribonuclease.
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__TOC__
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</StructureSection>
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==About this Structure==
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1YT3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA].
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==Reference==
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Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing., Zuo Y, Wang Y, Malhotra A, Structure. 2005 Jul;13(7):973-84. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16004870 16004870]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Ribonuclease III]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Malhotra A]]
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[[Category: Malhotra, A.]]
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[[Category: Wang Y]]
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[[Category: Wang, Y.]]
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[[Category: Zuo Y]]
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[[Category: Zuo, Y.]]
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[[Category: exonuclease]]
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[[Category: exoribonuclease]]
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[[Category: hydrolase]]
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[[Category: nuclease]]
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[[Category: ribonuclease]]
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[[Category: rnase]]
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[[Category: trna processing]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:21:36 2008''
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Current revision

Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing

PDB ID 1yt3

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