Article

Structural basis for DNA recognition and loading into a viral packaging motor

York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom.
Proceedings of the National Academy of Sciences (Impact Factor: 9.81). 12/2011; 109(3):811-6. DOI: 10.1073/pnas.1110270109
Source: PubMed

ABSTRACT Genome packaging into preformed viral procapsids is driven by powerful molecular motors. The small terminase protein is essential for the initial recognition of viral DNA and regulates the motor's ATPase and nuclease activities during DNA translocation. The crystal structure of a full-length small terminase protein from the Siphoviridae bacteriophage SF6, comprising the N-terminal DNA binding, the oligomerization core, and the C-terminal β-barrel domains, reveals a nine-subunit circular assembly in which the DNA-binding domains are arranged around the oligomerization core in a highly flexible manner. Mass spectrometry analysis and four further crystal structures show that, although the full-length protein exclusively forms nine-subunit assemblies, protein constructs missing the C-terminal β-barrel form both nine-subunit and ten-subunit assemblies, indicating the importance of the C terminus for defining the oligomeric state. The mechanism by which a ring-shaped small terminase oligomer binds viral DNA has not previously been elucidated. Here, we probed binding in vitro by using EPR and surface plasmon resonance experiments, which indicated that interaction with DNA is mediated exclusively by the DNA-binding domains and suggested a nucleosome-like model in which DNA binds around the outside of the protein oligomer.

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    • "The relationships between these more complete structures to the fragment structures of l and phage 44RR2 TerS structures are less clear (but see Gao and Rao, 2011). Nonetheless, in all of the TerS structures the N-terminal domain is largely helical and includes a helix-turn-helix motif that may be the DNA-binding portion of these proteins (Buttner et al., 2012; Roy et al., 2012; Zhao et al., 2012; Sun et al., 2012). Analysis of mutations of Sf6 TerS have indicated that its N-terminal domain is responsible for binding DNA nonspecifically in vitro (Zhao et al., 2010, 2012). "
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    • "Although octamers were also observed in solution for bacteriophage T7 (gp18) (White and Richardson, 1987) and T4 (gp16) (Lin et al., 1997) S-terminases, a recent crystal structure of the T4-like phage 44RR S-terminase (gp16) revealed a mix of undecamers and dodecamers (Sun et al., 2012). Similarly, phage SPP1 S-terminase (gp1) was reported to form decameric rings in solution (Camacho et al., 2003), but the crystal structure of the SPP1-like Bacillus phage SF6 revealed a mix of nonamers and decamers, with the nonamer being the predominant conformation (Bü ttner et al., 2012). Finally, phage l S-terminase (gpNu1) forms a hetero-trimer bound to a monomer of L-terminase (gpA1), and in vitro this protomer can further assemble into tetramers (Maluf et al., 2006). "
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