8DKR

Pseudomonas-phage E217 TerL nuclease domain

Summary for 8DKR

• Entry DOI: 10.2210/pdb8dkr/pdb
• Related: 4DKW
• Descriptor: Large terminase protein, MAGNESIUM ION (3 entities in total)
• Functional Keywords: viral genome packaging motor, large terminase, terl, pseudomonas phage e217, nuclease, hydrolase
• Biological source: Pseudomonas phage vB_PaeM_E217
• Total number of polymer chains: 2
• Total formula weight: 57047.83

Authors

Cingolani, G.,Lokareddy, R.,Hou, D. (deposition date: 2022-07-06, release date: 2022-09-07, Last modification date: 2023-10-18)

Primary citation

Lokareddy, R.K.,Hou, C.D.,Doll, S.G.,Li, F.,Gillilan, R.E.,Forti, F.,Horner, D.S.,Briani, F.,Cingolani, G.
Terminase Subunits from the Pseudomonas-Phage E217.
J.Mol.Biol., 434:167799-167799, 2022

PubMed Abstract: Pseudomonas phages are increasingly important biomedicines for phage therapy, but little is known about how these viruses package DNA. This paper explores the terminase subunits from the Myoviridae E217, a Pseudomonas-phage used in an experimental cocktail to eradicate P. aeruginosa in vitro and in animal models. We identified the large (TerL) and small (TerS) terminase subunits in two genes ∼58 kbs away from each other in the E217 genome. TerL presents a classical two-domain architecture, consisting of an N-terminal ATPase and C-terminal nuclease domain arranged into a bean-shaped tertiary structure. A 2.05 Å crystal structure of the C-terminal domain revealed an RNase H-like fold with two magnesium ions in the nuclease active site. Mutations in TerL residues involved in magnesium coordination had a dominant-negative effect on phage growth. However, the two ions identified in the active site were too far from each other to promote two-metal-ion catalysis, suggesting a conformational change is required for nuclease activity. We also determined a 3.38 Å cryo-EM reconstruction of E217 TerS that revealed a ring-like decamer, departing from the most common nonameric quaternary structure observed thus far. E217 TerS contains both N-terminal helix-turn-helix motifs enriched in basic residues and a central channel lined with basic residues large enough to accommodate double-stranded DNA. Overexpression of TerS caused a more than a 4-fold reduction of E217 burst size, suggesting a catalytic amount of the protein is required for packaging. Together, these data expand the molecular repertoire of viral terminase subunits to Pseudomonas-phages used for phage therapy.

PubMed: 36007626
DOI: 10.1016/j.jmb.2022.167799

Experimental method

X-RAY DIFFRACTION (2.05 Å)