Sandbox20: Difference between revisions
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==RTP== | ==RTP== | ||
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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===Structure of the RTP Dimer=== | ===Structure of the RTP Dimer=== | ||
[[Image:RTP Dimerisation.jpg | thumb | upright=1. | [[Image:RTP Dimerisation.jpg | thumb | upright=1.3| right| Polar interactions between α4 helices facilitates RTP 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>. | ||
The association of α4 helices into an antiparellel coiled coil leads to dimerisation (right). 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. The phenylalanine and tryptophan residues that form part of this network are shown in the image (below). The crystal structure of [[1bm9| RTP in its unbound state]] was determined in 1995. A [[1j0r| C110S mutant]] was then generated to prevent the aggregation of RTP through cysteine oxidation. With a very similar structure and almost no change in dimerisation and DNA-binding capacities, the mutant was the protein of choice for later studies. | |||
The association of α4 helices into an antiparellel coiled coil leads to dimerisation ( | |||
{| | |||
| [[Image:RTP 1 Symmetry.jpg | thumb | upright=1.5| right| Symmetry of the RTP dimer.]] | |||
| [[Image:Hydrophobic residues in RTP.jpg | thumb | upright=1.7| right| Hydrophobic surfaces within each RTP monomer support their conformation.]] | |||
|} | |||
===DNA Binding=== | ===DNA Binding=== | ||
