Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5 composed of 6 identical 90 kDa subunits is required for DNA replication. D5 consists of a primase domain flexibly attached to a hexameric C-terminal domain with confirmed nucleotide hydrolase and DNA-binding activity but an elusive helicase activity. We determined its structure by single-particle cryo-electron microscopy. It displays a helicase core flanked by N- and C-terminal domains. Model building was greatly helped by the predicted structure of the D5 monomer using AlphaFold2. The 3.5 Å structure of the N-terminal domain forms a well-defined tight ring while the resolution decreases towards the C-terminus still allowing the fit of the predicted structure. The N-terminal domain is the first structural representative of a D5_N domain in Pfam. Partially corresponding folds are found in papillomavirus E1 and polyomavirus LTA helicases. The helicase domain is very similar to the Pfam domain DUF5906 from the primase-helicase of phage NrS-1. Finally, the C-terminal domain yields the first structure of a Pfam Pox_D5 domain. Domains D5_N followed by DUF5906 and Pox_D5 have been identified with varying confidence in a family of proteins from large DNA viruses,bacteriophages and selfish DNA elements.

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