Phage P4 origin-binding domain structure reveals a mechanism for regulation of DNA-binding activity by homo- and heterodimerization of winged helix proteins.
The origin-binding domain of the gpalpha protein of phage P4 (P4-OBD) mediates origin recognition and regulation of gpalpha activity by the protein Cnr. We have determined the crystal structure of P4-OBD at 2.95 A resolution. The structure of P4-OBD is that of a dimer with pseudo twofold 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 locate to the dimer interface, indicating that Cnr acts by disrupting the gpalpha dimer. P4-OBD dimerization is mediated by helices alpha1 and alpha3 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 modelling. 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 heterodimerization scaffold.
Yeo
Hye-Jeong
HJ
Department of Biochemistry and Molecular Biophysics, Campus Box 8231, Washington University School of Medicine, 660 S. Euclid Ave., St Louis, MO 63110, USA.
Ziegelin
Günter
G
Korolev
Sergey
S
Calendar
Richard
R
Lanka
Erich
E
Waksman
Gabriel
G
D000595:Amino Acid Sequence; D001665:Binding Sites; D003090:Coliphages / Q000737:chemistry*; D003460:Crystallization; D004247:DNA / Q000378:metabolism; D004265:DNA Helicases / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D019281:Dimerization; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D012316:RNA Nucleotidyltransferases / Q000737:chemistry* / Q000378:metabolism; D018741:Replication Origin; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism; D014764:Viral Proteins / Q000737:chemistry* / Q000378:metabolism
C089636:Cnr protein, Bacteriophage P4; D004268:DNA-Binding Proteins; D014157:Transcription Factors; D014764:Viral Proteins; C095083:alpha protein, Bacteriophage P4; D004247:DNA; D012316:RNA Nucleotidyltransferases; D004265:DNA Helicases