SNAP output for PDB entry 7mkn [SNAP web server]

PDB-id

7mkn; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription-DNA-RNA

Method

cryo-EM (3.3 Å)

Summary

Escherichia coli RNA polymerase and rapa elongation complex

Reference

Qayyum MZ, Molodtsov V, Renda A, Murakami KS (2021): "Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli." J.Biol.Chem., 297, 101404. doi: 10.1016/j.jbc.2021.101404.

Abstract

After transcription termination, cellular RNA polymerases (RNAPs) are occasionally trapped on DNA, impounded in an undefined Post-Termination Complex (PTC), limiting the free RNAP pool and subsequently leading to inefficient transcription. In Escherichia coli, a Swi2/Snf2 family of ATPase called RapA is known to be involved in countering such inefficiency through RNAP recycling; however, the precise mechanism of this recycling is unclear. To better understand its mechanism, here we determined the structures of two sets of E. coli RapA-RNAP complexes, along with the RNAP core enzyme and the elongation complex (EC), using cryo-electron microscopy (cryo-EM). These structures revealed the large conformational changes of RNAP and RapA upon their association that has been implicated in the hindrance of PTC formation. Our results along with DNA binding assays reveal that although RapA binds RNAP away from the DNA-binding main channel, its binding can allosterically close the RNAP clamp, thereby preventing its non-specific DNA binding and PTC formation. Taken together, we propose that RapA acts as a guardian of RNAP by which RapA prevents non-specific DNA binding of RNAP without affecting the binding of promoter DNA recognition σ factor, thereby enhancing RNAP recycling.