The HTH motifs of the small subunit are necessary for pac site binding. They arrange in oligomeric circular arrays to bind to the DNA. The small terminase is an HTH-containing DNA-binding protein that has relevance in viral DNA recognition and switching between viral DNA replication and packaging.

DNA packaging in tailed bacteriophages and in evolutionarily related herpesviruses is controlled by a viral-encoded terminase. The terminase complex characterised in Bacillus subtilis bacteriophages SF6 and SPP1 consists of two proteins: G1P and G2P. The first three helices of G1P form the typical helix-turn-helix DNA-binding motif, which is followed by a fourth helix. The fourth helix acts as a linker between the DNA-binding domain and the oligomerisation domain PMID:23545641.

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site PMID:2679356. The small terminase protein is essential for the initial recognition of viral DNA and regulates the motor's ATPase and nuclease activities during DNA translocation PMID:22207627.

PFAM:PF03592,INTERPRO:IPR005335,DOI:10.1107/S1744309113004399,DOI:10.1073/pnas.1110270109,DOI:10.1093/nar/gkv1467