User:Karen Lee/Sandbox 1
From Proteopedia
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| - | + | ==Replication Termination== | |
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What is the significance of replication termination? Replication is an essential process in the cells of all living organisms. 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. | What is the significance of replication termination? Replication is an essential process in the cells of all living organisms. 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. | ||
| + | ==Structure of RTP== | ||
| - | + | <Structure load='1f4k' size='500' frame='true' align='right' caption='Crystal structure of the RTP/B-site DNA complex.' scene='Insert optional scene name here' /> | |
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| - | <Structure load='1f4k' size='500' frame='true' align='right' caption=' | + | |
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| + | RTP consists of four <scene name='User:Karen_Lee/Sandbox_1/Rtp_alpha_helices/1'>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. Of these elements, the <scene name='User:Karen_Lee/Sandbox_1/Rtp_alpha_helix_3_dna/1'>α3 helix</scene> inserts into the major groove of Ter DNA, the | ||
| + | <scene name='User:Karen_Lee/Sandbox_1/Rtp_beta_strand_dna/1'>β2 strand</scene> interacts with the minor groove and the N-terminal arm also binds to the Ter site. This was identified through site directed mutagenesis<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>. | ||
| + | ==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<ref>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.</ref>. 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<ref>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.</ref>. | ||
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| + | <Structure load='1ecr' size='500' frame='true' align='center' caption='Escherichia coli TUS complexed with DNA.' scene='User:Karen_Lee/Sandbox_1/Freeze_frame/1' /> | ||
| - | + | ==References== | |
| + | <references /> | ||
Revision as of 22:24, 7 May 2011
Contents |
Replication Termination
What is the significance of replication termination? Replication is an essential process in the cells of all living organisms. 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.
Structure of RTP
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RTP consists of four , three and an unstructured domain. Of these elements, the inserts into the major groove of Ter DNA, the interacts with the minor groove and the N-terminal arm also binds to the Ter site. This was identified through site directed mutagenesis[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].
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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.
