1wdu

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(New page: 200px<br /><applet load="1wdu" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wdu, resolution 2.4&Aring;" /> '''Endonuclease domain o...)
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[[Image:1wdu.gif|left|200px]]<br /><applet load="1wdu" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1wdu, resolution 2.4&Aring;" />
 
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'''Endonuclease domain of TRAS1, a telomere-specific non-LTR retrotransposon'''<br />
 
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==Overview==
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==Endonuclease domain of TRAS1, a telomere-specific non-LTR retrotransposon==
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The telomere-specific long interspersed nuclear element, TRAS1, encodes an, endonuclease domain, TRAS1-EN, which specifically cleaves the telomeric, repeat targets (TTAGG)n of insects and (TTAGGG)n of vertebrates. To, elucidate the sequence-specific recognition properties of TRAS1-EN, we, determined the crystal structure at 2.4-A resolution. TRAS1-EN has a, four-layered alpha/beta sandwich structure; its topology is similar to, apurinic/apyrimidinic endonucleases, but the beta-hairpin (beta10-beta11), at the edge of the DNA-binding surface makes an extra loop that, distinguishes TRAS1-EN from cellular apurinic/apyrimidinic endonucleases., A protein-DNA complex model suggests that the beta10-beta11 hairpin fits, into the minor groove, enabling interaction with the telomeric repeats., Mutational studies of TRAS1-EN also indicated that the Asp-130 and, beta10-beta11 hairpin structure are involved in specific recognition of, telomeric repeats.
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<StructureSection load='1wdu' size='340' side='right'caption='[[1wdu]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1wdu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bombyx_mori Bombyx mori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WDU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WDU FirstGlance]. <br>
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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]] 2.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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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=1wdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wdu OCA], [https://pdbe.org/1wdu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wdu RCSB], [https://www.ebi.ac.uk/pdbsum/1wdu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wdu ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q93139_BOMMO Q93139_BOMMO]
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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/wd/1wdu_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=1wdu ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The telomere-specific long interspersed nuclear element, TRAS1, encodes an endonuclease domain, TRAS1-EN, which specifically cleaves the telomeric repeat targets (TTAGG)n of insects and (TTAGGG)n of vertebrates. To elucidate the sequence-specific recognition properties of TRAS1-EN, we determined the crystal structure at 2.4-A resolution. TRAS1-EN has a four-layered alpha/beta sandwich structure; its topology is similar to apurinic/apyrimidinic endonucleases, but the beta-hairpin (beta10-beta11) at the edge of the DNA-binding surface makes an extra loop that distinguishes TRAS1-EN from cellular apurinic/apyrimidinic endonucleases. A protein-DNA complex model suggests that the beta10-beta11 hairpin fits into the minor groove, enabling interaction with the telomeric repeats. Mutational studies of TRAS1-EN also indicated that the Asp-130 and beta10-beta11 hairpin structure are involved in specific recognition of telomeric repeats.
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==About this Structure==
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Crystal structure of the endonuclease domain encoded by the telomere-specific long interspersed nuclear element, TRAS1.,Maita N, Anzai T, Aoyagi H, Mizuno H, Fujiwara H J Biol Chem. 2004 Sep 24;279(39):41067-76. Epub 2004 Jul 9. PMID:15247245<ref>PMID:15247245</ref>
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1WDU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bombyx_mori Bombyx mori] with PO4 and CL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WDU OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure of the endonuclease domain encoded by the telomere-specific long interspersed nuclear element, TRAS1., Maita N, Anzai T, Aoyagi H, Mizuno H, Fujiwara H, J Biol Chem. 2004 Sep 24;279(39):41067-76. Epub 2004 Jul 9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15247245 15247245]
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</div>
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<div class="pdbe-citations 1wdu" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Bombyx mori]]
[[Category: Bombyx mori]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Anzai, T.]]
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[[Category: Anzai T]]
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[[Category: Aoyagi, H.]]
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[[Category: Aoyagi H]]
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[[Category: Fujiwara, H.]]
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[[Category: Fujiwara H]]
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[[Category: Maita, N.]]
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[[Category: Maita N]]
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[[Category: Mizuno, H.]]
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[[Category: Mizuno H]]
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[[Category: CL]]
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[[Category: PO4]]
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[[Category: four-layered alpha/beta sandwich]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:48:17 2007''
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Current revision

Endonuclease domain of TRAS1, a telomere-specific non-LTR retrotransposon

PDB ID 1wdu

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