User:Nathan Harris/Tus: Difference between revisions

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=='''Structure of Tus protein and binding interactions with TerA'''==

{{STRUCTURE_1ecr| PDB=1ecr | SCENE=User:Nathan_Harris/Tus/Opening_scene/1}}

{{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 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 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 = "Kamada" /> <ref name = "Neylon />.

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 = "Kamada" /> <ref name = "Neylon" />.

=='''Confirmation changes induced on Ter sites'''==

The ''Ter'' region in ''E.coli'' between bases T5 and A9 is significantly underwound upon binding with Tus. This region of DNA is altered from standard B form which is attributed to straddling of ''Ter'' by interdomain β strands (βF and βG) and the L4 connecting loop of Tus. Tus interacts with ''Ter'' in a previously undescribed manner with β strands of Tus inserting almost perpendicularly into the major groove to recognise ''Ter''. Alteration of ''Ter'' is characterised by an extended major groove and a broadened minor groove generating an overall DNA bend of 20 degrees. Overall, contacts in these regions account for increased stability of the altered DNA shape and allow recognition of the appropriate ''Ter'' site.

The ''Ter'' region in ''E.coli'' between bases T5 and A9 is significantly underwound upon binding with Tus. This region of DNA is altered from standard B form which is attributed to straddling of ''Ter'' by interdomain β strands (βF and βG) and the L4 connecting loop of Tus. Tus interacts with ''Ter'' in a previously undescribed manner with β strands of Tus inserting almost perpendicularly into the major groove to recognise ''Ter''. Alteration of ''Ter'' is characterised by an extended major groove and a broadened minor groove generating an overall DNA bend of 20 degrees. Overall, contacts in these regions account for increased stability of the altered DNA shape and allow recognition of the appropriate ''Ter'' site <ref name = "Kamada" /> <ref name = "Neylon" />.

=='''Mechanism of action'''==

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@@ Line 11: / Line 11: @@
 =='''Structure of Tus protein and binding interactions with TerA'''==
-{{STRUCTURE_1ecr| PDB=1ecr | SCENE=User:Nathan_Harris/Tus/Opening_scene/1}}
+{{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 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 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 = "Kamada" /> <ref name = "Neylon />.
+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 = "Kamada" /> <ref name = "Neylon" />.
 =='''Confirmation changes induced on Ter sites'''==
-The ''Ter'' region in ''E.coli'' between bases T5 and A9 is significantly underwound upon binding with Tus. This region of DNA is altered from standard B form which is attributed to straddling of ''Ter'' by interdomain β strands (βF and βG) and the L4 connecting loop of Tus. Tus interacts with ''Ter'' in a previously undescribed manner with β strands of Tus inserting almost perpendicularly into the major groove to recognise ''Ter''. Alteration of ''Ter'' is characterised by an extended major groove and a broadened minor groove generating an overall DNA bend of 20 degrees. Overall, contacts in these regions account for increased stability of the altered DNA shape and allow recognition of the appropriate ''Ter'' site.
+The ''Ter'' region in ''E.coli'' between bases T5 and A9 is significantly underwound upon binding with Tus. This region of DNA is altered from standard B form which is attributed to straddling of ''Ter'' by interdomain β strands (βF and βG) and the L4 connecting loop of Tus. Tus interacts with ''Ter'' in a previously undescribed manner with β strands of Tus inserting almost perpendicularly into the major groove to recognise ''Ter''. Alteration of ''Ter'' is characterised by an extended major groove and a broadened minor groove generating an overall DNA bend of 20 degrees. Overall, contacts in these regions account for increased stability of the altered DNA shape and allow recognition of the appropriate ''Ter'' site <ref name = "Kamada" /> <ref name = "Neylon" />.
 =='''Mechanism of action'''==