Sandbox20: Difference between revisions

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Student, Craig T Martin, Michael Webster

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 <Structure load='2EFW' size='300' frame='true' align='right' caption='RTP' scene='Sandbox20/2efw/3' />
 [[Image:RTP a3 DNA binding.png | thumb | upright=1.2| left| DNA-binding interactions of the a3 helix of RTP.]]
--15 residues contribute to the attachment of an RTP molecule to the ''Ter'' DNA site. Most of this is contributed by the basic residues of the <scene name='Sandbox20/2efw/30'>α3 helix</scene>, which lies in the major groove of DNA.
-Herman's:
+When an RTP dimer binds to a TerA or TerB site, the basic residues of the a3 helix are positioned in the major grooven and the beta ribbon rests at the minor groove. Non-specific ionic interactions between the N-terminus and the DNA backbone stabilise the complex.
-When an RTP dimer binds to a TerA or TerB site, the basic residues of the a3 helix become positioned at the major groove and the beta ribbon rests at the minor groove. Non-specific ionic interactions between the N-terminus and the DNA backbone stabilise the complex.
 It is known, with some certainty, that the RTP dimer adopts an asymmetric arrangement upon binding of the TerB site. In the C110S mutant complexed with the native TerB sequence (2EFW), the two subunits interact differently with the DNA bases to produce wing-up and wing-down conformations. These can be distinguished by the angle the a2 helix makes with the a3 helix. It is likely that asymmetry is also introduced when the RTP dimer binds to the TerA site but the crystal structure of this complex has not been solved?
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 The asymmetry of the dimer is shown by the names 'wing up' and 'wing down'. It is measured by the angle between the a2 and a3 heices, as shown <scene name='Sandbox20/2efw/14'>by clicking here</scene>.
 === Replication Termination Activity===