2itl: Difference between revisions
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==The origin binding domain of the SV40 large T antigen bound to the functional pen palindrome DNA (23 bp)== | ==The origin binding domain of the SV40 large T antigen bound to the functional pen palindrome DNA (23 bp)== | ||
<StructureSection load='2itl' size='340' side='right' caption='[[2itl]], [[Resolution|resolution]] 1.65Å' scene=''> | <StructureSection load='2itl' size='340' side='right'caption='[[2itl]], [[Resolution|resolution]] 1.65Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2itl]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2itl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Macaca_mulatta_polyomavirus_1 Macaca mulatta polyomavirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ITL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ITL FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65Å</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=2itl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2itl OCA], [https://pdbe.org/2itl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2itl RCSB], [https://www.ebi.ac.uk/pdbsum/2itl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2itl ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/Q98ZP7_SV40 Q98ZP7_SV40] | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/it/2itl_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/it/2itl_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
| Line 29: | Line 28: | ||
</div> | </div> | ||
<div class="pdbe-citations 2itl" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 2itl" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Large T Antigen|Large T Antigen]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Macaca mulatta polyomavirus 1]] | ||
[[Category: | [[Category: Bochkarev A]] | ||
[[Category: Bochkareva E]] | |||
[[Category: | [[Category: Seitova A]] | ||
[[Category: | |||
Latest revision as of 13:16, 30 August 2023
The origin binding domain of the SV40 large T antigen bound to the functional pen palindrome DNA (23 bp)The origin binding domain of the SV40 large T antigen bound to the functional pen palindrome DNA (23 bp)
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori) in simian virus 40 (SV40). Here, we determined the crystal structures of the T-ag origin-binding domain (OBD) in apo form, and bound to either a 17 bp palindrome (sites 1 and 3) or a 23 bp ori DNA palindrome comprising all four GAGGC binding sites for OBD. The T-ag OBDs were shown to interact with the DNA through a loop comprising Ser147-Thr155 (A1 loop), a combination of a DNA-binding helix and loop (His203-Asn210), and Asn227. The A1 loop traveled back-and-forth along the major groove and accounted for most of the sequence-determining contacts with the DNA. Unexpectedly, in both T-ag-DNA structures, the T-ag OBDs bound DNA independently and did not make direct protein-protein contacts. The T-ag OBD was also captured bound to a non-consensus site ATGGC even in the presence of its canonical site GAGGC. Our observations taken together with the known biochemical and structural features of the T-ag-origin interaction suggest a model for origin unwinding. Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA.,Bochkareva E, Martynowski D, Seitova A, Bochkarev A EMBO J. 2006 Dec 13;25(24):5961-9. Epub 2006 Nov 30. PMID:17139255[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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