Sandbox20: Difference between revisions
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==RTP== | ==RTP== | ||
[[Image:RTP 1 Symmetry.jpg | thumb | upright=1.3| right| The two subunits of the RTP dimer complex.]] | |||
In B. subtilis, Ter sites are 30 bp in length with two imperfect inverted 16 bp repeats overlapping at a TAT motif. The upstream portion of the Ter site is called TerA; and the downstream portion, TerB. The sequence differences between these cause the bound RTP dimers to bind with different affinity and generate an assymetric complex capable of halting the progression of the replication fork only if the B site is encountered first.The mechanism by which this is achieved is discussed below in relation to the structure of the <scene name='Sandbox20/2efw/3'>RTP complex</scene>. | In B. subtilis, Ter sites are 30 bp in length with two imperfect inverted 16 bp repeats overlapping at a TAT motif. The upstream portion of the Ter site is called TerA; and the downstream portion, TerB. The sequence differences between these cause the bound RTP dimers to bind with different affinity and generate an assymetric complex capable of halting the progression of the replication fork only if the B site is encountered first.The mechanism by which this is achieved is discussed below in relation to the structure of the <scene name='Sandbox20/2efw/3'>RTP complex</scene>. | ||
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===The RTP Dimer=== | ===The RTP Dimer=== | ||
[[Image:RTP | [[Image:RTP Dimerisation.jpg | thumb | upright=1.1| left| Interactions between a4 helices facilitates dimerisation of RTP on the Ter DNA site.]] | ||
[[Image:Hydrophobic residues in RTP.jpg | thumb | upright=1.5| right| Hydrophobic surfaces within each RTP monomer support their conformation. The position of the α4 helix allows dimerisation.]] | |||
The structure of an RTP monomer bears greatest similarity to the "''classic winged-helix''" motif, in which 'wings' project from the loop between the final two β sheets of their compact αβααββ structure.<ref>PMID: 10679470</ref> The two major variations from this theme are the absence of a β1 sheet (the corresponding region is instead termed the β1 loop), and the presence of a fourth elongate α-helix at the C-terminus, which facilitates dimerisation. Each of these secondary structural elements are indicated in this <scene name='Sandbox20/2efw/8'>structure</scene>. | The structure of an RTP monomer bears greatest similarity to the "''classic winged-helix''" motif, in which 'wings' project from the loop between the final two β sheets of their compact αβααββ structure.<ref>PMID: 10679470</ref> The two major variations from this theme are the absence of a β1 sheet (the corresponding region is instead termed the β1 loop), and the presence of a fourth elongate α-helix at the C-terminus, which facilitates dimerisation. Each of these secondary structural elements are indicated in this <scene name='Sandbox20/2efw/8'>structure</scene>. | ||
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===DNA Binding=== | ===DNA Binding=== | ||
<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.]] | [[Image:RTP a3 DNA binding.png | thumb | upright=1.2| left| DNA-binding interactions of the a3 helix of RTP.]] | ||
13-15 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. | 13-15 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. | ||