User:Karen Lee/Sandbox 1
From Proteopedia
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==Structure of RTP== | ==Structure of RTP== | ||
| - | A single RTP monomer consists of four <scene name='User:Karen_Lee/Sandbox_1/Rtp_alpha_helices/ | + | A single RTP monomer consists of four <scene name='User:Karen_Lee/Sandbox_1/Rtp_alpha_helices/2'>α-helices</scene>, three <scene name='User:Karen_Lee/Sandbox_1/Rtp_beta_sheets/1'>β-strands</scene> and an unstructured |
<scene name='User:Karen_Lee/Sandbox_1/Rtp_n_terminal/1'>N-terminal</scene> domain. The <scene name='User:Karen_Lee/Sandbox_1/Rtp_alpha_helix_3_dna/1'>α3 helix</scene> binds to DNA by inserting into the major groove of Ter sites, while the | <scene name='User:Karen_Lee/Sandbox_1/Rtp_n_terminal/1'>N-terminal</scene> domain. The <scene name='User:Karen_Lee/Sandbox_1/Rtp_alpha_helix_3_dna/1'>α3 helix</scene> binds to DNA by inserting into the major groove of Ter sites, while the | ||
<scene name='User:Karen_Lee/Sandbox_1/Rtp_beta_strand_dna/1'>β2 strand</scene> interacts with the minor groove. The N-terminal arm also binds to the Ter site<ref>Pai, S. K., Bussiere, D. E., Wang, F., Hutchinson, C. A., White, S. W. & Bastia, D. (1996) The structure and function of the replication terminator protein of Bacillus subtilis: identification of the ‘winged helix’ DNA-binding domain. EMBO J. 15(12), 3164-3173.</ref>. | <scene name='User:Karen_Lee/Sandbox_1/Rtp_beta_strand_dna/1'>β2 strand</scene> interacts with the minor groove. The N-terminal arm also binds to the Ter site<ref>Pai, S. K., Bussiere, D. E., Wang, F., Hutchinson, C. A., White, S. W. & Bastia, D. (1996) The structure and function of the replication terminator protein of Bacillus subtilis: identification of the ‘winged helix’ DNA-binding domain. EMBO J. 15(12), 3164-3173.</ref>. | ||
Revision as of 06:04, 11 May 2011
Contents |
Replication Termination
Replication is an essential process in all cells. The process copies the chromosomal DNA of the organism to provide the extra copy needed in cell division and is therefore critical in the biological inheritance of genes. In cells with cicurlar chromosomes, replication starts from a simgle origin proceed with two replication forks moving in opposite directions. This process must be terminated, otherwise it would continue and multiple copies of the chromosome would be made.
The process of terminating replication is performed by replication termination proteins. These proteins bind to specific sequences in the DNA, called Ter sites. This binding provies a physical blockage in the DNA that stops the polymerase.
In each circular chromosome, there are two sets of Ter sites that appear roughly opposite to the origin of replication. One set blocks the clockwise replication fork while the other traps the anti-clockwise replication fork.
In B. subtilis, the termination protein is called Replication Terminator Protein (RTP), and in E. coli it is Termination Utilisation Substance (Tus).
RTP
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Structure of RTP
A single RTP monomer consists of four , three and an unstructured domain. The binds to DNA by inserting into the major groove of Ter sites, while the interacts with the minor groove. The N-terminal arm also binds to the Ter site[1].
Key Features of RTP
Two different RTP B sites have been found to interact with RTP. These are the symmetrical RTP B (sRB) site from TerI (the first Ter site that the clockwise replication fork encounters) and the native RTP B (nRB) site from TerI. These sequences differ only in 6 base pairs – three at the downstream end and three at the upstream end. The downstream changes have no bearing on the structure of RTP since the protein binds the downstream region in both sRB and nRB sequences with similar conformation. Additionally, no base-specific interactions are made in this region. However, the three upstream changes are all located in the major groove of the dsDNA. This is where the α3 helix binds which underlies RTP binding specificity[2]. Therefore, in binding of RTP monomers to the Ter site, there is a differential binding affinity in A and B sites, due to changes in the nRB site.
This leads into the fact that RTP binds asymmetrically across the nRB site and therefore allows the complex to act as a polar barrier to the replication fork. When the fork approaches the B site (with tight RTP-DNA binding) the fork is unable to progress and is paused. Approaching from the A site does not impede its progress. This polarity can be explained by both the differential binding affinity as explained above and the cooperative binding affect of the RTP monomers. The complex formed between an RTP molecule and the B site facilitates cooperative binding of another RTP monomer to the A site to form a complete RTP-Ter complex[3].
TUS
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Structure of Tus
References
- ↑ Pai, S. K., Bussiere, D. E., Wang, F., Hutchinson, C. A., White, S. W. & Bastia, D. (1996) The structure and function of the replication terminator protein of Bacillus subtilis: identification of the ‘winged helix’ DNA-binding domain. EMBO J. 15(12), 3164-3173.
- ↑ Vivian, J. P., Porter, C. J., Wilce, J. A. & Wilce, M. C. J. (2007) An Asymmetric Structure of the Bacillus subtilis Replication Terminator Protein in Complex with DNA. J. Mol. Biol. 370, 481-491.
- ↑ Vivian, J. P., Porter, C. J., Wilce, J. A. & Wilce, M. C. J. (2007) An Asymmetric Structure of the Bacillus subtilis Replication Terminator Protein in Complex with DNA. J. Mol. Biol. 370, 481-491.
