Fig. 4: Interactions between PtuA and Ec78 components in Ec78 structures.

a, Binding of msDNA to the central groove formed by PtuA. RT, PtuA and PtuB molecules are shown in surface representation. The other dimer of PtuAB is omitted for clarity. b, Superimposition of the Ec78 PtuA and the Septu PtuA (gray ribbons) structures reveals that unique protein elements in Ec78 PtuA evolved for contacting msDNA (m loop and helical flap) and the RT–ncRNA complex (N-terminal extension, NTE). The loop equivalent to the m loop in Septu PtuA would obstruct its ability to contact msDNA in the same manner. c, PtuA residues, mostly positively charged, making close contacts (within 3.5 Å) with the msDNA. Conservation of these residues is shown in Extended Data Fig. 5a. d, Close-up views illustrating structural features of PtuA interactions with the RT–ncRNA–msDNA tripartite. The characteristic domains of the RT are indicated and color coded. Nucleotides of the ncRNA and msDNA are labeled. NTE denotes the N-terminal extension of PtuA. Inset highlights the specific contacts of first α-helix of NTE with both the Finger and Thumb domains. e, The functional importance of msDNA-interacting residues. Left, phage challenge assay results with E. coli strain 11303 cells carrying an empty vector, the WT or mutant Ec78 in the msDNA-binding interface when challenged with serially diluted phage T5 phage (Source Data Fig. 4e). Right, cell growth arrest assay of the DH10 cells carrying an empty vector, the WT or mutant Ec78. f, Functional importance of the unique PtuA elements. Left, plaques challenge assay results with the E. coli strain 11303 cells carrying an empty vector, the wild-type (WT) or mutant Ec78 in PtuA when challenged with serially diluted phage T5 phage (Source Data Fig. 4f). Right, cell growth arrest assay of the DH10 cells carrying an empty vector, the wild-type (WT) or mutant Ec78. NTE denotes the N-terminal extension of PtuA; helical flap denodes the loop wrapping around the msDNA.

Source data