1KA8

Crystal Structure of the Phage P4 Origin-Binding Domain

Summary for 1KA8

• Entry DOI: 10.2210/pdb1ka8/pdb
• Descriptor: putative P4-specific DNA primase (2 entities in total)
• Functional Keywords: winged helix, transferase
• Biological source: Enterobacteria phage P4
• Total number of polymer chains: 6
• Total formula weight: 69847.85

Authors

Yeo, H.J.,Ziegelin, G.,Korolev, S.,Calendar, R.,Lanka, E.,Waksman, G. (deposition date: 2001-10-31, release date: 2002-04-17, Last modification date: 2024-02-07)

Primary citation

Yeo, H.J.,Ziegelin, G.,Korolev, S.,Calendar, R.,Lanka, E.,Waksman, G.
Phage P4 origin-binding domain structure reveals a mechanism for regulation of DNA-binding activity by homo- and heterodimerization of winged helix proteins.
Mol.Microbiol., 43:855-867, 2002

PubMed Abstract: 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.

PubMed: 11929537
DOI: 10.1046/j.1365-2958.2002.02796.x

Experimental method

X-RAY DIFFRACTION (2.95 Å)