7ssg

From Proteopedia

Mfd DNA complex

Structural highlights

7ssg is a 3 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 5.2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MFD_ECOLI Couples transcription and DNA repair by recognizing RNA polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent release of RNAP and its truncated transcript from the DNA, and recruitment of nucleotide excision repair machinery to the damaged site. Can also dissociate RNAP that is blocked by low concentration of nucleoside triphosphates or by physical obstruction, such as bound proteins. In addition, can rescue arrested complexes by promoting forward translocation. Has ATPase activity, which is required for removal of stalled RNAP, but seems to lack helicase activity. May act through a translocase activity that rewinds upstream DNA, leading either to translocation or to release of RNAP when the enzyme active site can not continue elongation.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

Elongation by RNA polymerase is dynamically modulated by accessory factors. The transcription-repair coupling factor (TRCF) recognizes paused/stalled RNAPs and either rescues transcription or initiates transcription termination. Precisely how TRCFs choose to execute either outcome remains unclear. With Escherichia coli as a model, we used single-molecule assays to study dynamic modulation of elongation by Mfd, the bacterial TRCF. We found that nucleotide-bound Mfd converts the elongation complex (EC) into a catalytically poised state, presenting the EC with an opportunity to restart transcription. After long-lived residence in this catalytically poised state, ATP hydrolysis by Mfd remodels the EC through an irreversible process leading to loss of the RNA transcript. Further, biophysical studies revealed that the motor domain of Mfd binds and partially melts DNA containing a template strand overhang. The results explain pathway choice determining the fate of the EC and provide a molecular mechanism for transcription modulation by TRCF.

Mechanism of transcription modulation by the transcription-repair coupling factor.,Paudel BP, Xu ZQ, Jergic S, Oakley AJ, Sharma N, Brown SHJ, Bouwer JC, Lewis PJ, Dixon NE, van Oijen AM, Ghodke H Nucleic Acids Res. 2022 Jun 10;50(10):5688-5712. doi: 10.1093/nar/gkac449. PMID:35641110^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations

reviews cite this structure

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References

↑ Selby CP, Sancar A. Molecular mechanism of transcription-repair coupling. Science. 1993 Apr 2;260(5104):53-8. PMID:8465200
↑ Selby CP, Sancar A. Structure and function of transcription-repair coupling factor. I. Structural domains and binding properties. J Biol Chem. 1995 Mar 3;270(9):4882-9. PMID:7876261
↑ Selby CP, Sancar A. Structure and function of transcription-repair coupling factor. II. Catalytic properties. J Biol Chem. 1995 Mar 3;270(9):4890-5. PMID:7876262
↑ Park JS, Marr MT, Roberts JW. E. coli Transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation. Cell. 2002 Jun 14;109(6):757-67. PMID:12086674
↑ Murphy MN, Gong P, Ralto K, Manelyte L, Savery NJ, Theis K. An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd. Nucleic Acids Res. 2009 Oct;37(18):6042-53. Epub 2009 Aug 21. PMID:19700770 doi:10.1093/nar/gkp680
↑ Paudel BP, Xu ZQ, Jergic S, Oakley AJ, Sharma N, Brown SHJ, Bouwer JC, Lewis PJ, Dixon NE, van Oijen AM, Ghodke H. Mechanism of transcription modulation by the transcription-repair coupling factor. Nucleic Acids Res. 2022 Jun 10;50(10):5688-5712. PMID:35641110 doi:10.1093/nar/gkac449