Sandbox20: Difference between revisions
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===DNA Binding=== | ===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. | 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. | ||
1. Interaction between the three β-sheets and the major groove of DNA involves both base-specific and base non-specific bonds. | 1. Interaction between the three β-sheets and the major groove of DNA involves both base-specific and base non-specific bonds. | ||
(<scene name='Sandbox20/Tus/19'>shown here</scene>). | (<scene name='Sandbox20/Tus/19'>shown here</scene>). | ||
{| | |||
| [[Image:Tus 2 DNA-binding domain.jpg|thumb|upright=1.3|Interaction between the beta sheet domain of Tus and the TerB DNA region.]] | |||
| [[Image:Tus-DNA polar contacts.jpg|thumb|upright|Base-specific polar contacts between the βJ strand and the major DNA groove.]] | |||
| [[Image:Tus-DNA nonpolar contacts.jpg|thumb|upright=1.4|Van der Waals and hydrophobic interactions between the βJ strand and the major DNA groove.]] | |||
|} | |||
2. | 2. | ||
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. | 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. | ||