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1t2t

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(New page: 200px<br /><applet load="1t2t" size="450" color="white" frame="true" align="right" spinBox="true" caption="1t2t, resolution 2.50&Aring;" /> '''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"
 
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caption="1t2t, resolution 2.50&Aring;" />
 
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'''Crystal structure of the DNA-binding domain of intron endonuclease I-TevI with operator site'''<br />
 
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==Overview==
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==Crystal structure of the DNA-binding domain of intron endonuclease I-TevI with operator site==
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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.
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<StructureSection load='1t2t' size='340' side='right'caption='[[1t2t]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<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>
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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]] 2.5&#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=ZN:ZINC+ION'>ZN</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=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>
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</table>
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== Function ==
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[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.
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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/t2/1t2t_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=1t2t 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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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.
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==About this Structure==
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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>
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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].
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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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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]
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</div>
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[[Category: Bacteriophage t4]]
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<div class="pdbe-citations 1t2t" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Belfort, M.]]
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[[Category: Boyd, T.M.]]
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[[Category: Derbyshire, V.]]
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[[Category: Edgell, D.R.]]
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[[Category: LaBonne, S.]]
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[[Category: Li, Z.]]
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[[Category: Roey, P.Van.]]
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[[Category: Shub, D.A.]]
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[[Category: Stanger, M.J.]]
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[[Category: ZN]]
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[[Category: protein-dna complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:56:44 2007''
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==See Also==
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Escherichia virus T4]]
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[[Category: Large Structures]]
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[[Category: Belfort M]]
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[[Category: Boyd TM]]
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[[Category: Derbyshire V]]
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[[Category: Edgell DR]]
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[[Category: LaBonne S]]
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[[Category: Li Z]]
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[[Category: Shub DA]]
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[[Category: Stanger MJ]]
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[[Category: Van Roey P]]

Current revision

Crystal structure of the DNA-binding domain of intron endonuclease I-TevI with operator site

PDB ID 1t2t

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