7cnb

Crystal structure of Gp16 C-terminal domain from Bacillus virus phi29Crystal structure of Gp16 C-terminal domain from Bacillus virus phi29

Structural highlights

7cnb is a 1 chain structure. Full crystallographic 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

Biological motors, ubiquitous in living systems, convert chemical energy into different kinds of mechanical motions critical to cellular functions. Gene product 16 (gp16) in bacteriophage varphi29 is among the most powerful biomotors known, which adopts a multisubunit ring-shaped structure and hydrolyzes ATP to package double-stranded DNA (dsDNA) into a preformed procapsid. Here we report the crystal structure of the C-terminal domain of gp16 (gp16-CTD). Structure-based alignment and molecular dynamics simulations revealed an essential binding surface of gp16-CTD for prohead RNA, a unique component of the motor complex. Furthermore, our simulations highlighted a dynamic interplay between the N-terminal domain and the CTD of gp16, which may play a role in driving movement of DNA into the procapsid. Lastly, we assembled an atomic structural model of the complete varphi29 dsDNA packaging motor complex by integrating structural and experimental data from multiple sources. Collectively, our findings provided a refined inchworm-revolution model for dsDNA translocation in bacteriophage varphi29 and suggested how the individual domains of gp16 work together to power such translocation.

Structural Insights into gp16 ATPase in the Bacteriophage varphi29 DNA Packaging Motor.,Saeed AFUH, Chan C, Guan H, Gong B, Guo P, Cheng X, Ouyang S Biochemistry. 2021 Mar 23;60(11):886-897. doi: 10.1021/acs.biochem.0c00935. Epub , 2021 Mar 9. PMID:33689296^[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
↑ Saeed AFUH, Chan C, Guan H, Gong B, Guo P, Cheng X, Ouyang S. Structural Insights into gp16 ATPase in the Bacteriophage varphi29 DNA Packaging Motor. Biochemistry. 2021 Mar 23;60(11):886-897. doi: 10.1021/acs.biochem.0c00935. Epub , 2021 Mar 9. PMID:33689296 doi:http://dx.doi.org/10.1021/acs.biochem.0c00935

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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] Saeed AFUH, Chan C, Guan H, Gong B, Guo P, Cheng X, Ouyang S. Structural Insights into gp16 ATPase in the Bacteriophage varphi29 DNA Packaging Motor. Biochemistry. 2021 Mar 23;60(11):886-897. doi: 10.1021/acs.biochem.0c00935. Epub , 2021 Mar 9. PMID:33689296 doi:http://dx.doi.org/10.1021/acs.biochem.0c00935

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