User:David McDonald/Replication Termination Protein: Difference between revisions
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The formation mechanism and subsequent structure this RTP-DNA complex has been a topic of some debate. Previously, it was thought that the complex was <scene name='User:David_McDonald/Replication_Termination_Protein/Symmetric_binding/3'> | The formation mechanism and subsequent structure this RTP-DNA complex has been a topic of some debate. Previously, it was thought that the complex was <scene name='User:David_McDonald/Replication_Termination_Protein/Symmetric_binding/3'>symmetric</scene><sup>[6]</sup>, with <scene name='User:David_McDonald/Replication_Termination_Protein/Symmetric_dna_interaction/1'>DNA interaction</scene> mediated by the α3 helix as predicted, but also the α1 helix and, surprisingly, the α1-α2 loop region. More specifically, the binding was attributed to <scene name='User:David_McDonald/Replication_Termination_Protein/Symmetric_interacting_residues/1'>residues</scene> | ||
Arg59, His54, Thr55 and Tyr58 of α3; Tyr33, Gly34 and Leu35 of α 1- α2 loop region and Gln15 of α1<sup>[6]</sup>. This structure was obtained with a symmetric B site analogue known as sRB as opposed to the wild type Ter sequence, which differs by 6 nucleotides. In particular, three modified upstream residues in sRB lie govern the overall interaction with the α3 helix. It is theorised that this changed interaction resulted in the initial, but incorrect, symmetric binding mode. <sup>[4]</sup> | Arg59, His54, Thr55 and Tyr58 of α3; Tyr33, Gly34 and Leu35 of α 1- α2 loop region and Gln15 of α1<sup>[6]</sup>. This structure was obtained with a symmetric B site analogue known as sRB as opposed to the wild type Ter sequence, which differs by 6 nucleotides. In particular, three modified upstream residues in sRB lie govern the overall interaction with the α3 helix. It is theorised that this changed interaction resulted in the initial, but incorrect, symmetric binding mode. <sup>[4]</sup> | ||
The observed symmetry was in contrast to the known polarity of the RTP-Ter site. Further research using the wild-type Ter sequence (nRB) revealed a distinct <scene name='User:David_McDonald/Replication_Termination_Protein/Asymmetric_binding/4'> | The observed symmetry was in contrast to the known polarity of the RTP-Ter site. Further research using the wild-type Ter sequence (nRB) revealed a distinct <scene name='User:David_McDonald/Replication_Termination_Protein/Asymmetric_binding/4'>asymmetry</scene> in both the RTP dimer and the DNA<sup>[4]</sup>. Although the interacting sequences remained the same, the downstream monomer displayed a <scene name='User:David_McDonald/Replication_Termination_Protein/Asymmetric_down/3'>"Wing down"</scene> confirmation, where the β2-loop-β3 structure makes contact with the phosphate backbone. Conversely, the upstream monomer displays a <scene name='User:David_McDonald/Replication_Termination_Protein/Asymmetric_up/2'>"Wing up"</scene> confirmation, with the wing making contact with the upstream minor groove. It is also proposed that interactions between these wings result in the co-operative binding properties of the Ter site.<sup>[4]</sup> | ||
[[Image:ABSiteImage-1-.PNG]] | [[Image:ABSiteImage-1-.PNG]] | ||
