4DYR

Crystal structure of terminase small subunit gp1 of the bacterial virus sf6 with CAPS PH10.5 buffer

Summary for 4DYR

• Entry DOI: 10.2210/pdb4dyr/pdb
• Related: 3HEF 4DYC 4DYQ 4DZJ 4DZP
• Descriptor: Gene 1 protein (2 entities in total)
• Functional Keywords: gp1, octamer, dna-binding, caps buffer, viral protein
• Biological source: Shigella phage Sf6 (Shigella flexneri bacteriophage VI)
• Total number of polymer chains: 2
• Total formula weight: 31153.56

Authors

Zhao, H.,Tang, L. (deposition date: 2012-02-29, release date: 2012-10-17, Last modification date: 2024-03-13)

Primary citation

Zhao, H.,Kamau, Y.N.,Christensen, T.E.,Tang, L.
Structural and Functional Studies of the Phage Sf6 Terminase Small Subunit Reveal a DNA-Spooling Device Facilitated by Structural Plasticity.
J.Mol.Biol., 423:413-426, 2012

PubMed Abstract: In many DNA viruses, genome packaging is initiated by the small subunit of the packaging terminase, which specifically binds to the packaging signal on viral DNA and directs assembly of the terminase holoenzyme. We have experimentally mapped the DNA-interacting region on Shigella virus Sf6 terminase small subunit gp1, which occupies extended surface areas encircling the gp1 octamer, indicating that DNA wraps around gp1 through extensive contacts. High-resolution structures reveal large-scale motions of the gp1 DNA-binding domain mediated by the curved helix formed by residues 54-81 and an intermolecular salt bridge formed by residues Arg67 and Glu73, indicating remarkable structural plasticity underlying multivalent, pleomorphic gp1:DNA interactions. These results provide spatial restraints for protein:DNA interactions, which enable construction of a three-dimensional pseudo-atomic model for a DNA-packaging initiation complex assembled from the terminase small subunit and the packaging region on viral DNA. Our results suggest that gp1 functions as a DNA-spooling device, which may transform DNA into a specific architecture appropriate for interaction with and cleavage by the terminase large subunit prior to DNA translocation into viral procapsid. This may represent a common mechanism for the initiation step of DNA packaging in tailed double-stranded DNA bacterial viruses.

PubMed: 22858866
DOI: 10.1016/j.jmb.2012.07.016

Experimental method

X-RAY DIFFRACTION (1.65 Å)