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The vaccinia virus early transcription factor (VETF) is an ATP-dependent activator of the early class of viral genes. VETF is a heterodimeric protein that binds an initiator-like element surrounding the start site of transcription. Previous studies indicated that the small subunit of VETF contacts the promoter DNA. We have taken a mutational approach to determine sequences in the VETF small subunit that are important for DNA binding. Two types of sequences were targeted for mutation: ones resembling motifs that are conserved in the nucleic acid helicase family and positively charged residues in predicted alpha-helices. Mutations affecting transcription activation were clustered in two regions. One mutation that impaired DNA binding is located near the N-terminus within the putative ATP-binding pocket that comprises helicase domain I. DNA binding was also severely reduced by mutations in a sequence resembling helicase domain VI and two putative alpha-helices that flank this domain in the C-terminal third of the polypeptide. These results indicate that the DNA binding domain in the small subunit of VETF is not isolated within a separable domain as is the case with most transcription factors, but rather, spans most of the length of the 637 residue polypeptide. A model for VETF structure is suggested in which the active site for ATP hydrolysis is integrated within an extended DNA-binding domain such that the structure and function of each domain influences that of the other.

The DNA binding domain of the vaccinia virus early transcription factor small subunit is an extended helicase-like motif