Protein Family Models

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]. 28100693. 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. [2]. 26150523. 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. (from Pfam)

Date:

2024-10-16

Terminase large subunit (TerL) from bacteriophages and evolutionarily related viruses, is an important component of the DNA packing machinery and comprises an ATPase domain, which powers DNA translocation and a nuclease domain that cuts concatemeric DNA [1,2]. TerL forms pentamers in which the ATPase domains form a ring distal to the capsid. This is the ATPase domain which contains a C-terminal subdomain that sits above the ATPase active site, called the "Lid subdomain" with reference to analogous lid subdomains found in other ATPases [3]. It contains a hydrophobic patch (Trp and Tyr residues) that mediates critical interactions in the interface between adjacent ATPase subunits and assists the positioning of the arginine finger residue that catalyses ATP hydrolysis [2,3]. This entry also includes bacterial proteins of unknown function. [1]. 7812447. Sequence and organization of the lactococcal prolate-headed bIL67 phage genome. Schouler C, Ehrlich SD, Chopin MC;. Microbiology 1994;140:3061-3069. [2]. 28100693. 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. [3]. 26150523. 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. (from Pfam)

Date:

2024-10-16

phage terminase large subunit may be involved in headful cutting of double-stranded concatemeric phage DNA and may be ATP-dependent

Date:

2024-12-05