User:Nathan Harris/Tus: Difference between revisions

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{{STRUCTURE_1ecr| PDB=1ecr | SCENE=User:Nathan_Harris/Tus/Opening_scene/1}}Tus constitutes 308 amino acids and a mass of approximately 36 kDa. The structural components of Tus have been elucidated through crystal structures of Tus bound to <scene name='User:Nathan_Harris/Tus/Ter/1'>TerA</scene> <ref name = "Kamada" />. Tus exhibits a unique binding motif to Ter sites previously undescribed from any known protein-DNA interactions.

Tus is divided into an <scene name='User:Nathan_Harris/Tus/Amino_domian/1'>amino domain</scene> and <scene name='User:Nathan_Harris/Tus/Carboxy_domain/1'>carboxy domain</scene> distinguished by two alpha helical regions and central β sheets combining to encompass a large central basic cleft. The <scene name='User:Nathan_Harris/Tus/Interdomain/2'>interdomain region</scene> consists of anti-parallel β strands and an <scene name='User:Nathan_Harris/Tus/L4/1'>extended L4 loop</scene> which connect the amino and carboxy domains. Within this interdomain region, the <scene name='User:Nathan_Harris/Tus/Bf/1'>βF</scene>, <scene name='User:Nathan_Harris/Tus/Bg/1'>βG</scene>, <scene name='User:Nathan_Harris/Tus/Bh/1'>βH</scene> and <scene name='User:Nathan_Harris/Tus/Bi/1'>βI</scene> strands are responsible for specific and non-specific recognition of ''Ter''.

The amino domain consists of three amphipathic alpha helices forming an anti-parallel bundle roughly parallel to ''Ter'', a sandwich of anti-parallel β sheets and three loops. The major groove and minor groove are clamped by two alpha helices (<scene name='User:Nathan_Harris/Tus/A4/1'>αIV</scene> and <scene name='User:Nathan_Harris/Tus/A5/1'>αV</scene>) which also contribute to the hydrophobic core of the protein. Within the β sandwich, <scene name='User:Nathan_Harris/Tus/Bcadke/1'>βCADKE</scene> contacts the alpha helical region, whereas <scene name='User:Nathan_Harris/Tus/Blfij/1'>βLFIJ</scene> is associated with DNA binding. Furthermore, the extended L4 loop is also involved in contacts to the minor groove.

The amino domain consists of three amphipathic alpha helices forming an anti-parallel bundle roughly parallel to ''Ter'', a sandwich of anti-parallel β sheets and three loops. The major groove and minor groove are clamped by two alpha helices (<scene name='User:Nathan_Harris/Tus/A4/1'>αIV</scene> and <scene name='User:Nathan_Harris/Tus/A5/1'>αV</scene>) which also contribute to the hydrophobic core of the protein. Within the β sandwich, <scene name='User:Nathan_Harris/Tus/Bcadke/2'>βCADKE</scene> contacts the alpha helical region, whereas <scene name='User:Nathan_Harris/Tus/Blfij/1'>βLFIJ</scene> is associated with DNA binding. Furthermore, the extended L4 loop is also involved in contacts to the minor groove.

The carboxy domain consists of a hydrophobic core stabilised by alpha helices and β strands (βGHNO). The <scene name='User:Nathan_Harris/Tus/L3/1'>L3 loop</scene> is responsible for connecting helices <scene name='User:Nathan_Harris/Tus/A6/1'>αVI</scene> and <scene name='User:Nathan_Harris/Tus/A7/1'>αVII</scene> and also contacts the minor groove of DNA <ref name = "Neylon" /><ref name = "Kamada" />.

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with Tus leading to dissociation of Tus and progression of the replication fork.

However, when ''E. coli'' ''Ter'' sequences are inserted into a plasmid in ''B. Subtillis'' expressing Tus, the replication fork arrest from the non-permissive

end only occurs with 0.5% efficiency compared to 45.4% efficiency in a wild type ''E. coli'' system<ref name = "Anderson"> Anderson, P., Griffith, A., Duggin, I. and Wake, R. (2000) Functional specificity of the replication fork-arrest complexes of Bacillus subtilis and Escherichia coli: significant specificity for Tus-Ter functioning in E.coli. Molecular Microbiology, 36 (6): 1327-1335.</ref>. If only Tus-''Ter'' interactions were important in the

end only occurs with 0.5% efficiency compared to 45.4% efficiency in a wild type ''E. coli'' system <ref name = "Anderson"> Anderson, P., Griffith, A., Duggin, I. and Wake, R. (2000) Functional specificity of the replication fork-arrest complexes of Bacillus subtilis and Escherichia coli: significant specificity for Tus-Ter functioning in E.coli. Molecular Microbiology, 36 (6): 1327-1335.</ref>. If only Tus-''Ter'' interactions were important in the

mediation of polar fork arrest, then the efficiency in the two systems should be similar. This highlights the importance of other factors in the

mediation of polar fork arrest.

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 {{STRUCTURE_1ecr| PDB=1ecr | SCENE=User:Nathan_Harris/Tus/Opening_scene/1}}Tus constitutes 308 amino acids and a mass of approximately 36 kDa. The structural components of Tus have been elucidated through crystal structures of Tus bound to <scene name='User:Nathan_Harris/Tus/Ter/1'>TerA</scene> <ref name = "Kamada" />. Tus exhibits a unique binding motif to Ter sites previously undescribed from any known protein-DNA interactions.
 Tus is divided into an <scene name='User:Nathan_Harris/Tus/Amino_domian/1'>amino domain</scene> and <scene name='User:Nathan_Harris/Tus/Carboxy_domain/1'>carboxy domain</scene> distinguished by two alpha helical regions and central β sheets combining to encompass a large central basic cleft. The <scene name='User:Nathan_Harris/Tus/Interdomain/2'>interdomain region</scene> consists of anti-parallel β strands and an <scene name='User:Nathan_Harris/Tus/L4/1'>extended L4 loop</scene> which connect the amino and carboxy domains. Within this interdomain region, the <scene name='User:Nathan_Harris/Tus/Bf/1'>βF</scene>, <scene name='User:Nathan_Harris/Tus/Bg/1'>βG</scene>, <scene name='User:Nathan_Harris/Tus/Bh/1'>βH</scene> and <scene name='User:Nathan_Harris/Tus/Bi/1'>βI</scene> strands are responsible for specific and non-specific recognition of ''Ter''.
-The amino domain consists of three amphipathic alpha helices forming an anti-parallel bundle roughly parallel to ''Ter'', a sandwich of anti-parallel β sheets and three loops. The major groove and minor groove are clamped by two alpha helices (<scene name='User:Nathan_Harris/Tus/A4/1'>αIV</scene> and <scene name='User:Nathan_Harris/Tus/A5/1'>αV</scene>) which also contribute to the hydrophobic core of the protein. Within the β sandwich, <scene name='User:Nathan_Harris/Tus/Bcadke/1'>βCADKE</scene> contacts the alpha helical region, whereas <scene name='User:Nathan_Harris/Tus/Blfij/1'>βLFIJ</scene> is associated with DNA binding.  Furthermore, the extended L4 loop is also involved in contacts to the minor groove.
+The amino domain consists of three amphipathic alpha helices forming an anti-parallel bundle roughly parallel to ''Ter'', a sandwich of anti-parallel β sheets and three loops. The major groove and minor groove are clamped by two alpha helices (<scene name='User:Nathan_Harris/Tus/A4/1'>αIV</scene> and <scene name='User:Nathan_Harris/Tus/A5/1'>αV</scene>) which also contribute to the hydrophobic core of the protein. Within the β sandwich, <scene name='User:Nathan_Harris/Tus/Bcadke/2'>βCADKE</scene> contacts the alpha helical region, whereas <scene name='User:Nathan_Harris/Tus/Blfij/1'>βLFIJ</scene> is associated with DNA binding.  Furthermore, the extended L4 loop is also involved in contacts to the minor groove.
 The carboxy domain consists of a hydrophobic core stabilised by alpha helices and β strands (βGHNO). The <scene name='User:Nathan_Harris/Tus/L3/1'>L3 loop</scene> is responsible for connecting helices <scene name='User:Nathan_Harris/Tus/A6/1'>αVI</scene> and <scene name='User:Nathan_Harris/Tus/A7/1'>αVII</scene> and also contacts the minor groove of DNA <ref name = "Neylon" /><ref name = "Kamada" />.
@@ Line 35: / Line 35: @@
 with Tus leading to dissociation of Tus and progression of the replication fork.
 However, when ''E. coli'' ''Ter'' sequences are inserted into a plasmid in ''B. Subtillis'' expressing Tus, the replication fork arrest from the non-permissive
-end only occurs with 0.5% efficiency compared to 45.4% efficiency in a wild type ''E. coli'' system<ref name = "Anderson"> Anderson, P., Griffith, A., Duggin, I. and Wake, R.  (2000) Functional specificity of the replication fork-arrest complexes of Bacillus subtilis and Escherichia coli: significant specificity for Tus-Ter functioning in E.coli.  Molecular Microbiology, 36 (6): 1327-1335.</ref>. If only Tus-''Ter'' interactions were important in the
+end only occurs with 0.5% efficiency compared to 45.4% efficiency in a wild type ''E. coli'' system <ref name = "Anderson"> Anderson, P., Griffith, A., Duggin, I. and Wake, R.  (2000) Functional specificity of the replication fork-arrest complexes of Bacillus subtilis and Escherichia coli: significant specificity for Tus-Ter functioning in E.coli.  Molecular Microbiology, 36 (6): 1327-1335.</ref>. If only Tus-''Ter'' interactions were important in the
 mediation of polar fork arrest, then the efficiency in the two systems should be similar. This highlights the importance of other factors in the
 mediation of polar fork arrest.