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[[Image:2itj.jpg|left|200px]]
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{{STRUCTURE_2itj|  PDB=2itj  |  SCENE=  }}
'''Origin binding domain of the SV40 large T antigen (residues 131-259). P212121 crystal form'''


==Origin binding domain of the SV40 large T antigen (residues 131-259). P212121 crystal form==
<StructureSection load='2itj' size='340' side='right'caption='[[2itj]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2itj]] is a 2 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=2ITJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ITJ 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2itj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2itj OCA], [https://pdbe.org/2itj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2itj RCSB], [https://www.ebi.ac.uk/pdbsum/2itj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2itj ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q98ZP7_SV40 Q98ZP7_SV40]
== 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/it/2itj_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=2itj ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The 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.


==Overview==
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<ref>PMID:17139255</ref>
The 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.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2ITJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Simian_virus_40 Simian virus 40]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ITJ OCA].
</div>
<div class="pdbe-citations 2itj" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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:[http://www.ncbi.nlm.nih.gov/pubmed/17139255 17139255]
*[[Large T Antigen|Large T Antigen]]
[[Category: Simian virus 40]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Bochkarev, A.]]
__TOC__
[[Category: Bochkareva, E.]]
</StructureSection>
[[Category: Martynowski, D.]]
[[Category: Large Structures]]
[[Category: Dna binding protein]]
[[Category: Macaca mulatta polyomavirus 1]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 07:51:07 2008''
[[Category: Bochkarev A]]
[[Category: Bochkareva E]]
[[Category: Martynowski D]]

Latest revision as of 10:16, 30 August 2023

Origin binding domain of the SV40 large T antigen (residues 131-259). P212121 crystal form

2itj, resolution 2.50Å

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