SNAP output for PDB entry 8xvb [SNAP web server]

PDB-id

8xvb; SNAP-derived features in text and JSON formats; DNAproDB

Class

viral protein-DNA

Method

cryo-EM (3.4 Å)

Summary

cryo-EM structure of atp-DNA-mub filaments

Reference

Zhao X, Gao Y, Gong Q, Zhang K, Li S (2024): "Elucidating the Architectural dynamics of MuB filaments in bacteriophage Mu DNA transposition." Nat Commun, 15, 6445. doi: 10.1038/s41467-024-50722-1.

Abstract

MuB is a non-specific DNA-binding protein and AAA+ ATPase that significantly influences the DNA transposition process of bacteriophage Mu, especially in target DNA selection for transposition. While studies have established the ATP-dependent formation of MuB filament as pivotal to this process, the high-resolution structure of a full-length MuB protomer and the underlying molecular mechanisms governing its oligomerization remain elusive. Here, we use cryo-EM to obtain a 3.4-Å resolution structure of the ATP(+)-DNA(+)-MuB helical filament, which encapsulates the DNA substrate within its axial channel. The structure categorizes MuB within the initiator clade of the AAA+ protein family and precisely locates the ATP and DNA binding sites. Further investigation into the oligomeric states of MuB show the existence of various forms of the filament. These findings lead to a mechanistic model where MuB forms opposite helical filaments along the DNA, exposing potential target sites on the bare DNA and then recruiting MuA, which stimulates MuB's ATPase activity and disrupts the previously formed helical structure. When this happens, MuB generates larger ring structures and dissociates from the DNA.