Transcription-repair coupling factor

The initial scene (switch to ) shows the domains of Mfd in the conformation of the apo-enzyme.^[2] The UvrA interaction site (on domain 2) is occluded by domain 7. The translocase domains (domain 5 and domain 6), through interactions with domains 1 and 3, are locked in an inactive conformation, preventing the typical hinge motion of translocases when they bind and hydrolyze ATP while moving along DNA. When Mfd binds to DNA in the presence of ADP·AlFₓ, Mfd undergoes large domain rearrangements, giving a hint how it might bind to stalled RNAP.^[3] A first glimpse of the Mfd RNAP complex was through cryo-EM, but large parts of the Mfd protein were not resolved.^[4]

In 2021, the structures of several intermediates in the presences of stalled RNAP were determined using cryo-EM, shedding further light on the loading and activation mechanism, as well as how translocation of Mfd on DNA leads to disruption of the RNAP elongation complex and recruitment of UvrA.^[5] When , the RID (domain 4) binds to the beta subunit of RNA polymerase and domains 5 and domain 6 bind to DNA and ATP. These multiple binding events require a different relative orientation of RID and the translocase domains, and the necessary conformational changes disrupt inter-domain interactions seen in the apo-structure while activating the translocase activity of Mfd.

Once the translocase domains are activated, they move closer and closer to the surface of the RNA polymerase in multiple cycles of ATP hydrolysis until . The translocase moving along the DNA together with the RID tethered at a fixed point on the RNAP surface result in substantial reorganization of the domain contacts and relative orientation. Eventually, this leads to the the , thus recruiting the NER machinery to the damaged template strand for subsequent repair. Further translocation (not shown) will lead to distabilization of the RNAP: nucleic acid complex, helping to dislodge the stalled RNAP. The changing domain contacts are schematically summarized below.

Distinct domain contacts in various Mfd structures

One of the functions of the large conformational change is to create a topological lock around the DNA to support translocation in a highly processive manner. Whereas in other systems, motor protein, clamp and clamp loader are separate proteins, all these functions are housed here in a single polypeptide. Mfd uses a single ATPase activity to create a sliding clamp and load it onto the DNA. The necessary reorganization of domains is visualized in a . ^[6]

In the apo-structure, domains 3 and 4 are far apart from each other (connected by an extended linker), but they make direct contacts when Mfd is loaded on DNA. On the other hand, domains 4 and 5 make direct contacts in the apo-structure, but are far apart from each other (coonected by an extended linker) when Mfd is loaded on DNA. Finally, domain 2 and domain 7 bind to each other in the apo-state whereas domain 2 is available for binding UvrA in the DNA-bound state.

3D Structures of Transcription-repair coupling factor

Transcription-repair coupling factor 3D structures

References

1. ↑ Selby CP. Mfd Protein and Transcription-Repair Coupling in Escherichia coli. Photochem Photobiol. 2017 Jan;93(1):280-295. doi: 10.1111/php.12675. Epub 2017, Jan 18. PMID:27864884 doi:http://dx.doi.org/10.1111/php.12675
2. ↑ Deaconescu AM, Chambers AL, Smith AJ, Nickels BE, Hochschild A, Savery NJ, Darst SA. Structural basis for bacterial transcription-coupled DNA repair. Cell. 2006 Feb 10;124(3):507-20. PMID:16469698 doi:10.1016/j.cell.2005.11.045
3. ↑ Brugger C, Zhang C, Suhanovsky MM, Kim DD, Sinclair AN, Lyumkis D, Deaconescu AM. Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd. Nat Commun. 2020 Jul 27;11(1):3740. doi: 10.1038/s41467-020-17457-1. PMID:32719356 doi:http://dx.doi.org/10.1038/s41467-020-17457-1
4. ↑ Shi J, Wen A, Zhao M, Jin S, You L, Shi Y, Dong S, Hua X, Zhang Y, Feng Y. Structural basis of Mfd-dependent transcription termination. Nucleic Acids Res. 2020 Nov 18;48(20):11762-11772. doi: 10.1093/nar/gkaa904. PMID:33068413 doi:http://dx.doi.org/10.1093/nar/gkaa904
5. ↑ Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA. Structural basis for transcription complex disruption by the Mfd translocase. Elife. 2021 Jan 22;10. pii: 62117. doi: 10.7554/eLife.62117. PMID:33480355 doi:http://dx.doi.org/10.7554/eLife.62117
6. ↑ The Storymorph Jmol scripts were used to create the interpolation shown in the morph. Coordinates available on Proteopedia