This is the endonuclease domain of Terminase large subunit TerL [1,2], a key component of the DNA packing machinery in tailed bacteriophages and related viruses. TerL comprises a N-terminal ATPase domain (Pfam:PF03354) which powers the DNA translocation and this C-terminal endonuclease domain that cuts concatemeric DNA first in the initiation phase in a sequence specific site and later in the completion stage of the DNA packaging process when the capsid is full [1,2]. Cryo-EM studies indicate that TerL forms a pentamer that binds to a dodecameric assembly called portal and attaches to the capsid. It has been proposed that nuclease domains form a radially arranged ring that is proximal to portal, playing a key role in pentamer assembly [2]. This nuclease domain has a RNAse H-like fold and it has been proposed to utilise a two-metal catalysis mechanism like in other RNAse H-like endonucleases such as RNase H, transposases, retroviral integrases and RuvC Holliday junction resolvases [1].

1: Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism. Xu RG, Jenkins HT, Chechik M, Blagova EV, Lopatina A, Klimuk E, Minakhin L, Severinov K, Greive SJ, Antson AA; Nucleic Acids Res. 2017;45:3580-3590. PMID:28100693

2: Structure and mechanism of the ATPase that powers viral genome packaging. Hilbert BJ, Hayes JA, Stone NP, Duffy CM, Sankaran B, Kelch BA; Proc Natl Acad Sci U S A. 2015;112:E3792-E3799. PMID:26150523