4IEE

Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6 complexed with ATP-r-S

Summary for 4IEE

• Entry DOI: 10.2210/pdb4iee/pdb
• Related: 4IDH 4IEI 4IFE
• Descriptor: Gene 2 protein, MAGNESIUM ION, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER, ... (4 entities in total)
• Functional Keywords: dna packaging, terminase, atpase, nuclease, atp-r-s binding, magnesium binding, viral protein
• Biological source: Shigella phage Sf6 (Shigella flexneri bacteriophage VI)
• Total number of polymer chains: 1
• Total formula weight: 55795.05

Authors

Zhao, H.,Christensen, T.,Kamau, Y.,Tang, L. (deposition date: 2012-12-13, release date: 2013-05-01, Last modification date: 2023-09-20)

Primary citation

Zhao, H.,Christensen, T.E.,Kamau, Y.N.,Tang, L.
Structures of the phage Sf6 large terminase provide new insights into DNA translocation and cleavage.
Proc.Natl.Acad.Sci.USA, 110:8075-8080, 2013

PubMed Abstract: Many DNA viruses use powerful molecular motors to cleave concatemeric viral DNA into genome-length units and package them into preformed procapsid powered by ATP hydrolysis. Here we report the structures of the DNA-packaging motor gp2 of bacteriophage Sf6, which reveal a unique clade of RecA-like ATPase domain and an RNase H-like nuclease domain tethered by a regulatory linker domain, exhibiting a strikingly distinct domain arrangement. The gp2 structures complexed with nucleotides reveal, at the atomic detail, the catalytic center embraced by the ATPase domain and the linker domain. The gp2 nuclease activity is modulated by the ATPase domain and is stimulated by ATP. An extended DNA-binding surface is formed by the linker domain and the nuclease domain. These results suggest a unique mechanism for translation of chemical reaction into physical motion of DNA and provide insights into coordination of DNA translocation and cleavage in a viral DNA-packaging motor, which may be achieved via linker-domain-mediated interdomain communication driven by ATP hydrolysis.

PubMed: 23630261
DOI: 10.1073/pnas.1301133110

Experimental method

X-RAY DIFFRACTION (1.89 Å)