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. 1996 Dec;5(12):2485–2493. doi: 10.1002/pro.5560051211

Crystal structure of the coat protein from the GA bacteriophage: model of the unassembled dimer.

C Z Ni 1, C A White 1, R S Mitchell 1, J Wickersham 1, R Kodandapani 1, D S Peabody 1, K R Ely 1
PMCID: PMC2143325  PMID: 8976557

Abstract

There are four groups of RNA bacteriophages with distinct antigenic and physicochemical properties due to differences in surface residues of the viral coat proteins. Coat proteins also play a role as translational repressor during the viral life cycle, binding an RNA hairpin within 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 A 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, Valegård K, Fridborg K, Liljas L. 1993, J Mol Biol 234:620-639) or as an unassembled dimer (Ni Cz, Syed R, Kodandapani R. Wickersham J, Peabody DS, Ely 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 129 amino acid residues. Sequence differences that contribute to distinct immunological and physical properties of the proteins are found at the surface of the intact virus in the AB and FG loops. There are six differences in potential RNA contact residues within the RNA-binding site located in an antiparallel beta-sheet across the dimer interface. Three 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 molecular genetics to define RNA-binding specificity by GA or MS2 coat protein (Lim F. Spingola M, Peabody DS, 1994, J Biol Chem 269:9006-9010). This sequence difference reflects recognition of the nucleotide at position -5 in the unpaired loop of the translational operators bound by these coat proteins. In GA, the nucleotide at this position is a purine whereas in MS2, it is a pyrimidine.

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Selected References

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  1. Adhin M. R., Hirashima A., van Duin J. Nucleotide sequence from the ssRNA bacteriophage JP34 resolves the discrepancy between serological and biophysical classification. Virology. 1989 May;170(1):238–242. doi: 10.1016/0042-6822(89)90371-1. [DOI] [PubMed] [Google Scholar]
  2. Beckett D., Uhlenbeck O. C. Ribonucleoprotein complexes of R17 coat protein and a translational operator analog. J Mol Biol. 1988 Dec 20;204(4):927–938. doi: 10.1016/0022-2836(88)90052-6. [DOI] [PubMed] [Google Scholar]
  3. Bernardi A., Spahr P. F. Nucleotide sequence at the binding site for coat protein on RNA of bacteriophage R17. Proc Natl Acad Sci U S A. 1972 Oct;69(10):3033–3037. doi: 10.1073/pnas.69.10.3033. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Berzin V., Avots A., Jansone I., Gintnere L., Tsimanis A. Sequence of the genes coding for the A-protein and coat protein of bacteriophage fr. Nucleic Acids Res. 1987 Aug 25;15(16):6741–6741. doi: 10.1093/nar/15.16.6741. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Brünger A. T. Crystallographic refinement by simulated annealing. Application to a 2.8 A resolution structure of aspartate aminotransferase. J Mol Biol. 1988 Oct 5;203(3):803–816. doi: 10.1016/0022-2836(88)90211-2. [DOI] [PubMed] [Google Scholar]
  6. Golmohammadi R., Fridborg K., Bundule M., Valegård K., Liljas L. The crystal structure of bacteriophage Q beta at 3.5 A resolution. Structure. 1996 May 15;4(5):543–554. doi: 10.1016/s0969-2126(96)00060-3. [DOI] [PubMed] [Google Scholar]
  7. Golmohammadi R., Valegård K., Fridborg K., Liljas L. The refined structure of bacteriophage MS2 at 2.8 A resolution. J Mol Biol. 1993 Dec 5;234(3):620–639. doi: 10.1006/jmbi.1993.1616. [DOI] [PubMed] [Google Scholar]
  8. Gott J. M., Wilhelm L. J., Uhlenbeck O. C. RNA binding properties of the coat protein from bacteriophage GA. Nucleic Acids Res. 1991 Dec 11;19(23):6499–6503. doi: 10.1093/nar/19.23.6499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hendrickson W. A. Stereochemically restrained refinement of macromolecular structures. Methods Enzymol. 1985;115:252–270. doi: 10.1016/0076-6879(85)15021-4. [DOI] [PubMed] [Google Scholar]
  10. Inokuchi Y., Takahashi R., Hirose T., Inayama S., Jacobson A. B., Hirashima A. The complete nucleotide sequence of the group II RNA coliphage GA. J Biochem. 1986 Apr;99(4):1169–1180. doi: 10.1093/oxfordjournals.jbchem.a135580. [DOI] [PubMed] [Google Scholar]
  11. Liljas L., Fridborg K., Valegård K., Bundule M., Pumpens P. Crystal structure of bacteriophage fr capsids at 3.5 A resolution. J Mol Biol. 1994 Dec 2;244(3):279–290. doi: 10.1006/jmbi.1994.1729. [DOI] [PubMed] [Google Scholar]
  12. Lim F., Peabody D. S. Mutations that increase the affinity of a translational repressor for RNA. Nucleic Acids Res. 1994 Sep 11;22(18):3748–3752. doi: 10.1093/nar/22.18.3748. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lim F., Spingola M., Peabody D. S. Altering the RNA binding specificity of a translational repressor. J Biol Chem. 1994 Mar 25;269(12):9006–9010. [PubMed] [Google Scholar]
  14. Merritt E. A., Murphy M. E. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D Biol Crystallogr. 1994 Nov 1;50(Pt 6):869–873. doi: 10.1107/S0907444994006396. [DOI] [PubMed] [Google Scholar]
  15. Ni C. Z., Syed R., Kodandapani R., Wickersham J., Peabody D. S., Ely K. R. Crystal structure of the MS2 coat protein dimer: implications for RNA binding and virus assembly. Structure. 1995 Mar 15;3(3):255–263. doi: 10.1016/S0969-2126(01)00156-3. [DOI] [PubMed] [Google Scholar]
  16. Peabody D. S., Ely K. R. Control of translational repression by protein-protein interactions. Nucleic Acids Res. 1992 Apr 11;20(7):1649–1655. doi: 10.1093/nar/20.7.1649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Stockley P. G., Stonehouse N. J., Murray J. B., Goodman S. T., Talbot S. J., Adams C. J., Liljas L., Valegård K. Probing sequence-specific RNA recognition by the bacteriophage MS2 coat protein. Nucleic Acids Res. 1995 Jul 11;23(13):2512–2518. doi: 10.1093/nar/23.13.2512. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Stonehouse N. J., Stockley P. G. Effects of amino acid substitution on the thermal stability of MS2 capsids lacking genomic RNA. FEBS Lett. 1993 Nov 22;334(3):355–359. doi: 10.1016/0014-5793(93)80711-3. [DOI] [PubMed] [Google Scholar]
  19. Stonehouse N. J., Valegård K., Golmohammadi R., van den Worm S., Walton C., Stockley P. G., Liljas L. Crystal structures of MS2 capsids with mutations in the subunit FG loop. J Mol Biol. 1996 Feb 23;256(2):330–339. doi: 10.1006/jmbi.1996.0089. [DOI] [PubMed] [Google Scholar]
  20. Valegård K., Murray J. B., Stockley P. G., Stonehouse N. J., Liljas L. Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature. 1994 Oct 13;371(6498):623–626. doi: 10.1038/371623a0. [DOI] [PubMed] [Google Scholar]
  21. Van Assche W., Vandekerckhove J., Van Montagu M. Mutation sites in the coat-protein gene of bacteriophage MS2. Arch Int Physiol Biochim. 1974 Dec;82(5):1020–1021. [PubMed] [Google Scholar]
  22. Weber K. Amino acid sequence studies on the tryptic peptides of the coat protein of the bacteriophage R17. Biochemistry. 1967 Oct;6(10):3144–3154. doi: 10.1021/bi00862a023. [DOI] [PubMed] [Google Scholar]
  23. Wittmann-Liebold B., Wittmann H. G. Coat proteins of strains of two RNA viruses: comparison of their amino acid sequences. Mol Gen Genet. 1967;100(4):358–363. doi: 10.1007/BF00334062. [DOI] [PubMed] [Google Scholar]

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