CRYSTAL-STRUCTURE OF THE COAT PROTEIN FROM THE GA BACTERIOPHAGE - MODEL OF THE UNASSEMBLED DIMER

There are four groups of RNA bacteriophages with distinct antigenic an d physicochemical properties due to differences in surface residues of the viral coat proteins. Coat proteins also play a role as translatio nal repressor during the viral life cycle, binding an RNA hairpin with in the genome. In this study, the first crystal structure of the coat protein from a Group II phage GA is reported and compared to the Group I MS2 coat protein. The structure of the GA dimer was determined at 2 .8 Angstrom resolution (R-factor = 0.20). The overall folding pattern of the coat protein is similar to the Group I MS2 coat protein in the intact virus (Golmohammadi R, Valegard K, Fridborg K, Liljas L, 1993, J Mol Biol 234:620-639) or as an unassembled dimer(Ni CZ, Syed R, Koda ndapani R, Wickersham J, Peabody DS, Ply KR, 1995, Structure 3:255-263 ). The structures differ in the FG loops and in the first turn of the alpha A helix. GA and MS2 coat proteins differ in sequence at 49 of 12 9 amino acid residues. Sequence differences that contribute to distinc t immunological and physical properties of the proteins are found at t he surface of the intact virus in the AB and FG loops. There are six d ifferences in potential RNA contact residues within the RNA-binding si te located in an antiparallel beta-sheet across the dimer interface. T hree differences involve residues in the center of this concave site: Lys/Arg 83, Ser/Asn 87, and Asp/Glu 89. Residue 87 was shown by molecu lar genetics to define RNA-binding specificity by GA or MS2 coat prote in (Lim F, Spingola M, Peabody DS, 1994, J Biol Chem 269:9006-9010). T his sequence difference reflects recognition of the nucleotide at posi tion -5 in the unpaired loop of the translational operators bound by t hese coat proteins. In GA, the nucleotide at this position is a purine whereas in MS2, it is a pyrimidine.