RTP and Tus: Difference between revisions
No edit summary |
No edit summary |
||
| Line 12: | Line 12: | ||
[[Image:1BM9.2.jpg|300px|left|thumb| First determined RTP structure. By Bussiere ''et al.'' (PDB entry 1BM9) ]][[Image:1ECR.jpg|300px|right|thumb| Tus-Ter complex]] | |||
| Line 41: | Line 41: | ||
<Structure load='1F4K' size='400' frame='true' align='left' caption='RTP complexed with ''Ter''DNA' (Wilce ''et al.'', 2001)' scene='RTP_and_Tus/Practice_structure/1' /> | |||
== RTP: A homodimer responsible for polar arrest == | == RTP: A homodimer responsible for polar arrest == | ||
The first crystal structure of the Replicator Terminator Protein (RTP) from ''Bacillus subtilis'' was determined in 1995 by Bussiere ''et al.'' <ref>Bussiere DE, Bastia D, White SW (1995) Crystal structure of the replication terminator protein from ''B. subtilis'' at 2.6 A. ''Cell'' 80(4): 651-60.</ref>. | The first crystal structure of the Replicator Terminator Protein (RTP) from ''Bacillus subtilis'' was determined in 1995 by Bussiere ''et al.'' (See figure above) <ref>Bussiere DE, Bastia D, White SW (1995) Crystal structure of the replication terminator protein from ''B. subtilis'' at 2.6 A. ''Cell'' 80(4): 651-60.</ref>. This analysis revealed that RTP is comprised of two identical monomers, each of which binds to DNA to form a homodimer. The separate monomers bind at 30 bp sequences known as the A and B termination (Ter) sites. Both of these sites have inverted 16 bp repeats which overlap at highly conserved TAT trinucleotide sequence. This first structure, which used a symmetric B Ter DNA homologue, suggested that the RTP exists as a symmetric homodimer. The idea that a symmetric protein structure could be responsible for an inherently polar mechanism has resulted in a series of proposed solutions and discoveries regarding the mechanism of replication fork arrest. | ||
<scene name='RTP_and_Tus/Practice_structure/1'>Practice</scene> | <scene name='RTP_and_Tus/Practice_structure/1'>Practice</scene> | ||
| Line 69: | Line 62: | ||
The idea that RTP binds with differing affinity to the A and B Ter sites has since been explained on a molecular level with the determination of the crystal structure of RTP while bound to its native B Ter site by Vivian ''et al.'', 2007. This structure differed from that found by Bussiere ''et al.'' in that it used RTP bound to the native B Ter site, which is asymmetric, as opposed to a symmetric homologue. This revealed both the protein and the Ter DNA are asymmetric, potentially explaining the differential binding affinities between the A and B Ter sites <ref>Vivian JP, Porter CJ, Wilce JA, Wilce MCJ (2007) An asymmetric structure of the ''Bacillus subtilis'' Replication Terminator Protein in complex with DNA. ''Journal of Molecular Biology'' 370: 481-491.</ref>. | The idea that RTP binds with differing affinity to the A and B Ter sites has since been explained on a molecular level with the determination of the crystal structure of RTP while bound to its native B Ter site by Vivian ''et al.'', 2007. This structure differed from that found by Bussiere ''et al.'' in that it used RTP bound to the native B Ter site, which is asymmetric, as opposed to a symmetric homologue. This revealed both the protein and the Ter DNA are asymmetric, potentially explaining the differential binding affinities between the A and B Ter sites <ref>Vivian JP, Porter CJ, Wilce JA, Wilce MCJ (2007) An asymmetric structure of the ''Bacillus subtilis'' Replication Terminator Protein in complex with DNA. ''Journal of Molecular Biology'' 370: 481-491.</ref>. | ||
The entire concept of a “molecular clamp” in fork arrest has since been refuted by mutational studies performed by Duggin ''et al.'' in 2004. After creating mutant DNA Ter sites and analysing the resulting efficiency of replication fork arrest, Duggin ''et al.'' found that mutations which caused decreased affinity of RTP for the proximal half of the terminator DNA (i.e. the half which faces the approaching replisome) did not necessarily decrease fork arrest efficiency, and that increased proximal site affinity did not increase fork arrest efficiency. These results were inconsistent with the differential binding affinity model and induced conformational change, suggesting other factors apart from DNA-protein binding must also be responsible for replication fork arrest by RTP <ref>Duggin IG, Matthews JM, Dixon, NE, Wake RG, Mackay JP (2004) A Complex Mechanism Determines Polarity of DNA Replication Fork Arrest by the Replication Terminator Complex of ''Bacillus subtilis''. ''The Journal of Biological Chemistry'' 280(13): 13105-13113.</ref>. | |||
| Line 91: | Line 83: | ||
<Structure load='2I06' size='400' frame='true' align='left' caption='Tus complexed with Ter DNA (Kamada ''et al'' 1996)' scene='Insert optional scene name here' /> | |||
== Tus: an asymmetric monomer, and unlikely candidate. == | == Tus: an asymmetric monomer, and unlikely candidate. == | ||