Phage P4 origin-binding domain structure reveals a mechanism for regulation of DNA-binding activity by homo- and hetero-dimerization of winged helix proteins

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The origin-binding domain of the gp-alpha protein of phage P4 (P4-OBD) mediates origin- recognition and regulation of gp-alpha activity by the protein Cnr. We have determined the crystal structure of P4-OBD at 2.95 Å resolution. The structure of P4-OBD is that of a dimer with pseudo 2-fold symmetry. Each subunit has a winged helix topology with a unique structure among initiator proteins. The only structural homologue of the P4-OBD subunit is the DNA-binding domain of the eukaryotic transcriptional activator Rfx1. Based on this structural alignment, a model for origin-recognition by the P4-OBD dimer is suggested. P4-OBD mutations that interfere with Cnr binding locates to the dimer interface, indicating that Cnr acts by disrupting the gp_ dimer. P4-OBD dimerization is mediated by helices 1 and 3 in both subunits, a mode of winged helix protein dimerization that is reminiscent of that of the eukaryotic transcription factors E2F and DP. This in turn suggests that Cnr is also a winged helix protein, a possibility that is supported by previously-unreported sequence homologies between Cnr and Rfx1 and homology modeling. Hence, in a mechanism that appears to be conserved from phage to man, the DNA-binding activity of winged helix proteins can be regulated by other winged helix proteins via the versatile use of the winged helix motif as a homo- or hetero-dimerization scaffold.

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