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New page: left|200px<br /><applet load="1t2t" size="450" color="white" frame="true" align="right" spinBox="true" caption="1t2t, resolution 2.50Å" /> '''Crystal structure of...
 
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[[Image:1t2t.gif|left|200px]]<br /><applet load="1t2t" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1t2t, resolution 2.50&Aring;" />
'''Crystal structure of the DNA-binding domain of intron endonuclease I-TevI with operator site'''<br />


==Overview==
==Crystal structure of the DNA-binding domain of intron endonuclease I-TevI with operator site==
Customary binding sites of intron-encoded homing endonucleases lie within, cognate intronless alleles, at the so-called homing sites. Here, we, describe a novel, high-affinity binding site for I-TevI endonuclease, encoded within the group I td intron of phage T4. This site is an operator, that overlaps the T4 late promoter, which drives I-TevI expression from, within the td intron. I-TevI binds the operator and homing sites with, equal affinity, and functions as a transcriptional autorepressor. Distinct, sequence and spacing requirements of the catalytic domain result in, reduced cleavage activity on operator DNA. Crystallographic studies showed, that the overall interactions of the DNA-binding domain with the operator, and homing sites are similar, but have some different hydrogen-bonding, contacts. We present a model in which the flexibility in protein-DNA, interactions allows I-TevI to bind variant intronless alleles to promote, intron mobility while facilitating its function in autorepression, and, thereby persistence in its host.
<StructureSection load='1t2t' size='340' side='right'caption='[[1t2t]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1t2t]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T2T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T2T 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]] 2.5&#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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1t2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t2t OCA], [https://pdbe.org/1t2t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t2t RCSB], [https://www.ebi.ac.uk/pdbsum/1t2t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t2t ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TEV1_BPT4 TEV1_BPT4] This endonuclease is specific to the thymidylate synthase (td) gene splice junction and is involved in intron homing.
== 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/t2/1t2t_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=1t2t ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Customary binding sites of intron-encoded homing endonucleases lie within cognate intronless alleles, at the so-called homing sites. Here, we describe a novel, high-affinity binding site for I-TevI endonuclease, encoded within the group I td intron of phage T4. This site is an operator that overlaps the T4 late promoter, which drives I-TevI expression from within the td intron. I-TevI binds the operator and homing sites with equal affinity, and functions as a transcriptional autorepressor. Distinct sequence and spacing requirements of the catalytic domain result in reduced cleavage activity on operator DNA. Crystallographic studies showed that the overall interactions of the DNA-binding domain with the operator and homing sites are similar, but have some different hydrogen-bonding contacts. We present a model in which the flexibility in protein-DNA interactions allows I-TevI to bind variant intronless alleles to promote intron mobility while facilitating its function in autorepression, and thereby persistence in its host.


==About this Structure==
Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor.,Edgell DR, Derbyshire V, Van Roey P, LaBonne S, Stanger MJ, Li Z, Boyd TM, Shub DA, Belfort M Nat Struct Mol Biol. 2004 Oct;11(10):936-44. Epub 2004 Sep 7. PMID:15361856<ref>PMID:15361856</ref>
1T2T is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1T2T OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor., Edgell DR, Derbyshire V, Van Roey P, LaBonne S, Stanger MJ, Li Z, Boyd TM, Shub DA, Belfort M, Nat Struct Mol Biol. 2004 Oct;11(10):936-44. Epub 2004 Sep 7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15361856 15361856]
</div>
[[Category: Bacteriophage t4]]
<div class="pdbe-citations 1t2t" style="background-color:#fffaf0;"></div>
[[Category: Single protein]]
[[Category: Belfort, M.]]
[[Category: Boyd, T.M.]]
[[Category: Derbyshire, V.]]
[[Category: Edgell, D.R.]]
[[Category: LaBonne, S.]]
[[Category: Li, Z.]]
[[Category: Roey, P.Van.]]
[[Category: Shub, D.A.]]
[[Category: Stanger, M.J.]]
[[Category: ZN]]
[[Category: protein-dna complex]]


''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:56:44 2007''
==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia virus T4]]
[[Category: Large Structures]]
[[Category: Belfort M]]
[[Category: Boyd TM]]
[[Category: Derbyshire V]]
[[Category: Edgell DR]]
[[Category: LaBonne S]]
[[Category: Li Z]]
[[Category: Shub DA]]
[[Category: Stanger MJ]]
[[Category: Van Roey P]]
Retrieved from "https://proteopedia.org/1t2t"