2nl8: Difference between revisions

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New page: left|200px<br /><applet load="2nl8" size="350" color="white" frame="true" align="right" spinBox="true" caption="2nl8, resolution 2.30Å" /> '''The origin binding d...
 
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[[Image:2nl8.gif|left|200px]]<br /><applet load="2nl8" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2nl8, resolution 2.30&Aring;" />
'''The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)'''<br />


==Overview==
==The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)==
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.
<StructureSection load='2nl8' size='340' side='right'caption='[[2nl8]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2nl8]] 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=2NL8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NL8 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]] 2.3&#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=2nl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nl8 OCA], [https://pdbe.org/2nl8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nl8 RCSB], [https://www.ebi.ac.uk/pdbsum/2nl8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nl8 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/nl/2nl8_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=2nl8 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2NL8 is a [http://en.wikipedia.org/wiki/Single_protein 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=2NL8 OCA].
*[[Large T Antigen|Large T Antigen]]
 
__TOC__
==Reference==
</StructureSection>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17139255 17139255]
[[Category: Large Structures]]
[[Category: Simian virus 40]]
[[Category: Macaca mulatta polyomavirus 1]]
[[Category: Single protein]]
[[Category: Bochkarev A]]
[[Category: Bochkarev, A.]]
[[Category: Bochkareva E]]
[[Category: Bochkareva, E.]]
[[Category: Martynowski D]]
[[Category: Martynowski, D.]]
[[Category: dna binding protein]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 20:55:42 2008''

Latest revision as of 09:28, 3 April 2024

The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)

Structural highlights

2nl8 is a 2 chain structure with sequence from Macaca mulatta polyomavirus 1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q98ZP7_SV40

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2nl8, resolution 2.30Å

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
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