Sandbox20: Difference between revisions

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===DNA Binding===

Tus is among the most stable monomeric, sequence-specific, double-stranded DNA-binding proteins. This is due to a combination of three major sets of interactions; base-specific polar interactions within the major groove, non-polar contacts with the carboxy domain, and a phosphate clamp within the amino domain. The three β-sheets which span the major groove of DNA make both base-specific and base non-specific bonds, as shown in <~~scenename~~='Sandbox20/Tus/19'>~~this~~ model</scene>. In particular, three glutamine residues on the βJ strand form bidentate hydrogen bonds to bases at the permissive end of the complex (below centre). Interspersed with these residues on the same strand, residues such as isoleucine make Van der Waals and hydrophobic interactions to sugar and base moieties (below right).

Tus is among the most stable monomeric, sequence-specific, double-stranded DNA-binding proteins. This is due to a combination of three major sets of interactions; base-specific polar interactions within the major groove, non-polar contacts with the carboxy domain, and a phosphate clamp within the amino domain. The three β-sheets which span the major groove of DNA make both base-specific and base non-specific bonds, as shown in this <scene name='Sandbox20/Tus/19'>model</scene>. In particular, three glutamine residues on the βJ strand form bidentate hydrogen bonds to bases at the permissive end of the complex (below centre). Interspersed with these residues on the same strand, residues such as isoleucine make Van der Waals and hydrophobic interactions to sugar and base moieties (below right). The distribution of bonds to each strand of the duplex is highly asymmetric, and one strand is largely exposed to the solvent. This contributes to allowing the passage of the fork from one side only.

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2.

The ''phosphate clamp'' is located at the end of the aIV and aV helices, closest to where the replication fork is stalled. <ref>pdb: 8857533</ref> It ensures the protein does not come loose at the critical end and allow helicase activity to occur. It involves five, mostly van der Waals, contacts with the sugar-phosphate backbone.

3. The phosphate clamp is located at the end of the aIV and aV helices, closest to where the replication fork is stalled. <ref>pdb: 8857533</ref> It ensures the protein does not come loose at the critical end and allow helicase activity to occur. It involves five, mostly van der Waals, contacts with the sugar-phosphate backbone.

===Replication Termination Activity===

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@@ Line 59: / Line 59: @@
 ===DNA Binding===
-Tus is among the most stable monomeric, sequence-specific, double-stranded DNA-binding proteins. This is due to a combination of three major sets of interactions; base-specific polar interactions within the major groove, non-polar contacts with the carboxy domain, and a phosphate clamp within the amino domain. The three β-sheets which span the major groove of DNA make both base-specific and base non-specific bonds, as shown in <scenename='Sandbox20/Tus/19'>this model</scene>. In particular, three glutamine residues on the βJ strand form bidentate hydrogen bonds to bases at the permissive end of the complex (below centre). Interspersed with these residues on the same strand, residues such as isoleucine make Van der Waals and hydrophobic interactions to sugar and base moieties (below right).
+Tus is among the most stable monomeric, sequence-specific, double-stranded DNA-binding proteins. This is due to a combination of three major sets of interactions; base-specific polar interactions within the major groove, non-polar contacts with the carboxy domain, and a phosphate clamp within the amino domain. The three β-sheets which span the major groove of DNA make both base-specific and base non-specific bonds, as shown in this <scene name='Sandbox20/Tus/19'>model</scene>. In particular, three glutamine residues on the βJ strand form bidentate hydrogen bonds to bases at the permissive end of the complex (below centre). Interspersed with these residues on the same strand, residues such as isoleucine make Van der Waals and hydrophobic interactions to sugar and base moieties (below right). The distribution of bonds to each strand of the duplex is highly asymmetric, and one strand is largely exposed to the solvent. This contributes to allowing the passage of the fork from one side only.
 {|
@@ Line 67: / Line 67: @@
 |}
-.
+The ''phosphate clamp'' is located at the end of the aIV and aV helices, closest to where the replication fork is stalled. <ref>pdb:  8857533</ref> It ensures the protein does not come loose at the critical end and allow helicase activity to occur. It involves five, mostly van der Waals, contacts with the sugar-phosphate backbone.
-. The phosphate clamp is located at the end of the aIV and aV helices, closest to where the replication fork is stalled. <ref>pdb:  8857533</ref> It ensures the protein does not come loose at the critical end and allow helicase activity to occur. It involves five, mostly van der Waals, contacts with the sugar-phosphate backbone.
 ===Replication Termination Activity===