Sandbox20: Difference between revisions
| Line 16: | Line 16: | ||
==RTP== | ==RTP== | ||
[[Image:RTP 1 Symmetry.jpg | thumb | upright=1.3| right]] | [[Image:RTP 1 Symmetry.jpg | thumb | upright=1.3| right| Symmetry of the RTP dimer.]] | ||
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>. | ||
| Line 23: | Line 23: | ||
===The RTP Dimer=== | ===The RTP Dimer=== | ||
[[Image:RTP Dimerisation.jpg | thumb | upright=1.1| left| Interactions between α4 helices facilitates dimerisation of RTP on the Ter DNA site.]] | [[Image:RTP Dimerisation.jpg | thumb | upright=1.1| left| Interactions between α4 helices facilitates dimerisation of RTP on the Ter DNA site.]] | ||
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>. | ||
[[Image:Hydrophobic residues in RTP.jpg | thumb | upright=1.5| right| Hydrophobic surfaces within each RTP monomer support their conformation.]] | |||
The association of α4 helices into an antiparellel coiled coil leads to dimerisation (left). The conformation is further stabilised by interhelical salt bridges outside this region, as well as an aromatic network on the inner surface which form a hydrophobic core (right). The phenylalanine and tryptophan residues that form part of this network are shown in the image. | The association of α4 helices into an antiparellel coiled coil leads to dimerisation (left). The conformation is further stabilised by interhelical salt bridges outside this region, as well as an aromatic network on the inner surface which form a hydrophobic core (right). The phenylalanine and tryptophan residues that form part of this network are shown in the image. | ||