6v1w

NMR Structure of C-terminal Domain of phi29 ATPaseNMR Structure of C-terminal Domain of phi29 ATPase

Structural highlights

6v1w is a 1 chain structure with sequence from Bacillus virus phi29. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PKG16_BPPH2 ATPase required for the genome encapsidation reaction. Part of the active packaging motor via the binding to the packaging RNA (pRNA), itself fixed to the head-tail connector at the unique portal vertex of the prohead. Binds and supercoils the DNA-gp3 to produce an initiation complex for DNA packaging. Provides the energy to actively pump the viral DNA into the prohead. Approximately one molecule of ATP is used in the packaging of 2 bp of viral DNA. After packaging, the ATPase and the pRNA are released from the prohead.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Double-stranded DNA viruses use ATP-powered molecular motors to package their genomic DNA. To ensure efficient genome encapsidation, these motors regulate functional transitions between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the bacteriophage phi29 ATPase (CTD) that suggest a structural basis for these functional transitions. Sedimentation experiments show that the inter-domain linker in the full-length protein promotes oligomerization and thus may play a role in assembly of the functional motor. The NMR solution structure of the CTD indicates it is a vestigial nuclease domain that likely evolved from conserved nuclease domains in phage terminases. Despite the loss of nuclease activity, fluorescence binding assays confirm the CTD retains its DNA binding capabilities and fitting the CTD into cryoEM density of the phi29 motor shows that the CTD directly binds DNA. However, the interacting residues differ from those identified by NMR titration in solution, suggesting that packaging motors undergo conformational changes to transition between initiation, translocation, and termination. Taken together, these results provide insight into the evolution of functional transitions in viral dsDNA packaging motors.

NMR structure of a vestigial nuclease provides insight into the evolution of functional transitions in viral dsDNA packaging motors.,Mahler BP, Bujalowski PJ, Mao H, Dill EA, Jardine PJ, Choi KH, Morais MC Nucleic Acids Res. 2020 Oct 21. pii: 5934415. doi: 10.1093/nar/gkaa874. PMID:33089330^[5]

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

References

↑ Simpson AA, Tao Y, Leiman PG, Badasso MO, He Y, Jardine PJ, Olson NH, Morais MC, Grimes S, Anderson DL, Baker TS, Rossmann MG. Structure of the bacteriophage phi29 DNA packaging motor. Nature. 2000 Dec 7;408(6813):745-50. PMID:11130079 doi:10.1038/35047129
↑ Koti JS, Morais MC, Rajagopal R, Owen BA, McMurray CT, Anderson DL. DNA packaging motor assembly intermediate of bacteriophage phi29. J Mol Biol. 2008 Sep 19;381(5):1114-32. doi: 10.1016/j.jmb.2008.04.034. Epub 2008, Apr 20. PMID:18674782 doi:http://dx.doi.org/10.1016/j.jmb.2008.04.034
↑ Guo P, Peterson C, Anderson D. Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage phi 29. J Mol Biol. 1987 Sep 20;197(2):229-36. doi: 10.1016/0022-2836(87)90121-5. PMID:2960820 doi:http://dx.doi.org/10.1016/0022-2836(87)90121-5
↑ Garvey KJ, Saedi MS, Ito J. The complete sequence of Bacillus phage phi 29 gene 16: a protein required for the genome encapsidation reaction. Gene. 1985;40(2-3):311-6. PMID:3879485
↑ Mahler BP, Bujalowski PJ, Mao H, Dill EA, Jardine PJ, Choi KH, Morais MC. NMR structure of a vestigial nuclease provides insight into the evolution of functional transitions in viral dsDNA packaging motors. Nucleic Acids Res. 2020 Oct 21. pii: 5934415. doi: 10.1093/nar/gkaa874. PMID:33089330 doi:http://dx.doi.org/10.1093/nar/gkaa874

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OCA

[1] Simpson AA, Tao Y, Leiman PG, Badasso MO, He Y, Jardine PJ, Olson NH, Morais MC, Grimes S, Anderson DL, Baker TS, Rossmann MG. Structure of the bacteriophage phi29 DNA packaging motor. Nature. 2000 Dec 7;408(6813):745-50. PMID:11130079 doi:10.1038/35047129

[2] Koti JS, Morais MC, Rajagopal R, Owen BA, McMurray CT, Anderson DL. DNA packaging motor assembly intermediate of bacteriophage phi29. J Mol Biol. 2008 Sep 19;381(5):1114-32. doi: 10.1016/j.jmb.2008.04.034. Epub 2008, Apr 20. PMID:18674782 doi:http://dx.doi.org/10.1016/j.jmb.2008.04.034

[3] Guo P, Peterson C, Anderson D. Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage phi 29. J Mol Biol. 1987 Sep 20;197(2):229-36. doi: 10.1016/0022-2836(87)90121-5. PMID:2960820 doi:http://dx.doi.org/10.1016/0022-2836(87)90121-5

[4] Garvey KJ, Saedi MS, Ito J. The complete sequence of Bacillus phage phi 29 gene 16: a protein required for the genome encapsidation reaction. Gene. 1985;40(2-3):311-6. PMID:3879485

[5] Mahler BP, Bujalowski PJ, Mao H, Dill EA, Jardine PJ, Choi KH, Morais MC. NMR structure of a vestigial nuclease provides insight into the evolution of functional transitions in viral dsDNA packaging motors. Nucleic Acids Res. 2020 Oct 21. pii: 5934415. doi: 10.1093/nar/gkaa874. PMID:33089330 doi:http://dx.doi.org/10.1093/nar/gkaa874

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