1i3j

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[[Image:1i3j.gif|left|200px]]
 
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<!--The below Structure Template creates the "Structure Box" on the page. It is automatically created and periodically refreshed. All changes to the Structure Template will be lost EXCEPT for changes in the PDB parameter (setting the PDB file loaded) or the SCENE parameter (setting the initial scene to display when the page is loaded). -->
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==CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH ITS SUBSTRATE==
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<!-- STRUCTURE TEMPLATE BEGIN -->
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<StructureSection load='1i3j' size='340' side='right'caption='[[1i3j]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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{{Structure
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== Structural highlights ==
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|PDB= 1i3j |SIZE=350|CAPTION= <scene name='initialview01'>1i3j</scene>, resolution 2.2&Aring;
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<table><tr><td colspan='2'>[[1i3j]] 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=1I3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I3J FirstGlance]. <br>
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|SITE=
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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]] 2.2&#8491;</td></tr>
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
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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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|ACTIVITY=
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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=1i3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i3j OCA], [https://pdbe.org/1i3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i3j RCSB], [https://www.ebi.ac.uk/pdbsum/1i3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i3j ProSAT]</span></td></tr>
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|GENE=
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</table>
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|DOMAIN=
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== Function ==
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|RELATEDENTRY=
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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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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1i3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i3j OCA], [http://www.ebi.ac.uk/pdbsum/1i3j PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1i3j RCSB]</span>
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== Evolutionary Conservation ==
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}}
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[[Image:Consurf_key_small.gif|200px|right]]
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<!-- STRUCTURE TEMPLATE END -->
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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/i3/1i3j_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=1i3j ConSurf].
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<div style="clear:both"></div>
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'''CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH ITS SUBSTRATE'''
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==See Also==
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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I-TevI is a site-specific, sequence-tolerant intron endonuclease. The crystal structure of the DNA-binding domain of I-TevI complexed with the 20 bp primary binding region of its DNA target reveals an unusually extended structure composed of three subdomains: a Zn finger, an elongated segment containing a minor groove-binding alpha-helix, and a helix-turn-helix. The protein wraps around the DNA, mostly following the minor groove, contacting the phosphate backbone along the full length of the duplex. Surprisingly, while the minor groove-binding helix and the helix-turn- helix subdomain make hydrophobic contacts, the few base-specific hydrogen bonds occur in segments that lack secondary structure and flank the intron insertion site. The multiple base-specific interactions over a long segment of the substrate are consistent with the observed high site specificity in spite of sequence tolerance, while the modular composition of the domain is pertinent to the evolution of homing endonucleases.
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[[Category: Escherichia virus T4]]
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[[Category: Large Structures]]
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==About this Structure==
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[[Category: Belfort M]]
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1I3J is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I3J OCA].
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[[Category: Derbyshire V]]
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[[Category: Fox KM]]
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==Reference==
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[[Category: Van Roey P]]
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Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate., Van Roey P, Waddling CA, Fox KM, Belfort M, Derbyshire V, EMBO J. 2001 Jul 16;20(14):3631-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11447104 11447104]
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[[Category: Waddling CA]]
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[[Category: Enterobacteria phage t4]]
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[[Category: Single protein]]
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[[Category: Belfort, M.]]
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[[Category: Derbyshire, V.]]
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[[Category: Fox, K M.]]
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[[Category: Roey, P Van.]]
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[[Category: Waddling, C A.]]
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[[Category: Extended structure]]
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[[Category: Helix-turn-helix]]
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[[Category: Minor groove helix]]
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[[Category: Protein-dna complex]]
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[[Category: Zn-finger]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Apr 7 20:48:26 2008''
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Current revision

CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH ITS SUBSTRATE

PDB ID 1i3j

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