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TitleThe Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction.
Journal, issue, pagesViruses, Vol. 14, Issue 10, Year 2022
Publish dateOct 7, 2022
AuthorsStephanie Hutin / Wai Li Ling / Nicolas Tarbouriech / Guy Schoehn / Clemens Grimm / Utz Fischer / Wim P Burmeister /
PubMed AbstractPoxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA ...Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA replication. D5 consists of a primase fragment flexibly attached to the hexameric C-terminal polypeptide (res. 323-785) 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 an AAA+ helicase core flanked by N- and C-terminal domains. Model building was greatly helped by the predicted structure of D5 using AlphaFold2. The 3.9 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 partially present in papillomavirus E1 and polyomavirus LTA helicases, as well as in a bacteriophage NrS-1 helicase domain, which is also closely related to the AAA+ helicase domain of D5. Using the Pfam domain database, a D5_N domain followed by DUF5906 and Pox_D5 domains could be assigned to the cryo-EM structure, providing the first 3D structures for D5_N and Pox_D5 domains. The same domain organization has been identified in a family of putative helicases from large DNA viruses, bacteriophages, and selfish DNA elements.
External linksViruses / PubMed:36298761 / PubMed Central
MethodsEM (single particle)
Resolution4.1 - 6.6 Å
Structure data

15574

8apl

EMDB-15574: Symmetric hexamer of vaccinia virus DNA helicase D5 residues 323-785
PDB-8apl: Vaccinia virus DNA helicase D5 residues 323-785 hexamer with bound DNA processed in C6
Method: EM (single particle) / Resolution: 4.1 Å

15575

8apm

EMDB-15575, PDB-8apm:
Vaccinia virus DNA helicase D5 residues 323-785 hexamer with bound DNA processed in C1
Method: EM (single particle) / Resolution: 6.6 Å

Source
  • vaccinia virus copenhagen
  • synthetic construct (others)
KeywordsVIRAL PROTEIN / DNA helicase / D5_N domain / DUF5906 domain / Pox_D5 domain / SF3 helicase

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