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. 1993 Mar;12(3):861–867. doi: 10.1002/j.1460-2075.1993.tb05726.x

OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences.

A G Murzin 1
PMCID: PMC413284  PMID: 8458342

Abstract

A novel folding motif has been observed in four different proteins which bind oligonucleotides or oligosaccharides: staphylococcal nuclease, anticodon binding domain of asp-tRNA synthetase and B-subunits of heat-labile enterotoxin and verotoxin-1. The common fold of the four proteins, which we call the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands. The barrel-helix frameworks can be superimposed with r.m.s. deviations of 1.4-2.2 A, but no similarities can be observed in the corresponding alignment of the four sequences. The nucleotide or sugar binding sites, known for three of the four proteins, are located in nearly the same position in each protein: on the side surface of the beta-barrel, where three loops come together. Here we describe the determinants of the OB-fold, based on an analysis of all four structures. These proposed determinants explain how very different sequences adopt the OB-fold. They also suggest a reinterpretation of the controversial structure of gene 5 ssDNA binding protein, which exhibits some topological and functional similarities with the OB-fold proteins.

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Selected References

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  1. Arnone A., Bier C. J., Cotton F. A., Day V. W., Hazen E. E., Jr, Richardson D. C., Yonath A., Richardson J. S. A high resolution structure of an inhibitor complex of the extracellular nuclease of Staphylococcus aureus. I. Experimental procedures and chain tracing. J Biol Chem. 1971 Apr 10;246(7):2302–2316. [PubMed] [Google Scholar]
  2. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  3. Brayer G. D., McPherson A. Refined structure of the gene 5 DNA binding protein from bacteriophage fd. J Mol Biol. 1983 Sep 15;169(2):565–596. doi: 10.1016/s0022-2836(83)80065-5. [DOI] [PubMed] [Google Scholar]
  4. Chothia C., Janin J. Orthogonal packing of beta-pleated sheets in proteins. Biochemistry. 1982 Aug 17;21(17):3955–3965. doi: 10.1021/bi00260a009. [DOI] [PubMed] [Google Scholar]
  5. Chothia C. Proteins. One thousand families for the molecular biologist. Nature. 1992 Jun 18;357(6379):543–544. doi: 10.1038/357543a0. [DOI] [PubMed] [Google Scholar]
  6. Folkers P. J., van Duynhoven J. P., Jonker A. J., Harmsen B. J., Konings R. N., Hilbers C. W. Sequence-specific 1H-NMR assignment and secondary structure of the Tyr41----His mutant of the single-stranded DNA binding protein, gene V protein, encoded by the filamentous bacteriophage M13. Eur J Biochem. 1991 Dec 5;202(2):349–360. doi: 10.1111/j.1432-1033.1991.tb16382.x. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Hynes T. R., Fox R. O. The crystal structure of staphylococcal nuclease refined at 1.7 A resolution. Proteins. 1991;10(2):92–105. doi: 10.1002/prot.340100203. [DOI] [PubMed] [Google Scholar]
  9. Jackson M. P., Wadolkowski E. A., Weinstein D. L., Holmes R. K., O'Brien A. D. Functional analysis of the Shiga toxin and Shiga-like toxin type II variant binding subunits by using site-directed mutagenesis. J Bacteriol. 1990 Feb;172(2):653–658. doi: 10.1128/jb.172.2.653-658.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Lesk A. M., Brändén C. I., Chothia C. Structural principles of alpha/beta barrel proteins: the packing of the interior of the sheet. Proteins. 1989;5(2):139–148. doi: 10.1002/prot.340050208. [DOI] [PubMed] [Google Scholar]
  11. Loll P. J., Lattman E. E. The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A. Proteins. 1989;5(3):183–201. doi: 10.1002/prot.340050302. [DOI] [PubMed] [Google Scholar]
  12. Lüthy R., Bowie J. U., Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992 Mar 5;356(6364):83–85. doi: 10.1038/356083a0. [DOI] [PubMed] [Google Scholar]
  13. McLachlan A. D. Gene duplications in the structural evolution of chymotrypsin. J Mol Biol. 1979 Feb 15;128(1):49–79. doi: 10.1016/0022-2836(79)90308-5. [DOI] [PubMed] [Google Scholar]
  14. Moras D. Structural and functional relationships between aminoacyl-tRNA synthetases. Trends Biochem Sci. 1992 Apr;17(4):159–164. doi: 10.1016/0968-0004(92)90326-5. [DOI] [PubMed] [Google Scholar]
  15. Morris A. L., MacArthur M. W., Hutchinson E. G., Thornton J. M. Stereochemical quality of protein structure coordinates. Proteins. 1992 Apr;12(4):345–364. doi: 10.1002/prot.340120407. [DOI] [PubMed] [Google Scholar]
  16. Murzin A. G., Lesk A. M., Chothia C. beta-Trefoil fold. Patterns of structure and sequence in the Kunitz inhibitors interleukins-1 beta and 1 alpha and fibroblast growth factors. J Mol Biol. 1992 Jan 20;223(2):531–543. doi: 10.1016/0022-2836(92)90668-a. [DOI] [PubMed] [Google Scholar]
  17. Perera L. P., Samuel J. E., Holmes R. K., O'Brien A. D. Identification of three amino acid residues in the B subunit of Shiga toxin and Shiga-like toxin type II that are essential for holotoxin activity. J Bacteriol. 1991 Feb;173(3):1151–1160. doi: 10.1128/jb.173.3.1151-1160.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Richardson J. S. The anatomy and taxonomy of protein structure. Adv Protein Chem. 1981;34:167–339. doi: 10.1016/s0065-3233(08)60520-3. [DOI] [PubMed] [Google Scholar]
  19. Richardson J. S. beta-Sheet topology and the relatedness of proteins. Nature. 1977 Aug 11;268(5620):495–500. doi: 10.1038/268495a0. [DOI] [PubMed] [Google Scholar]
  20. Ruff M., Krishnaswamy S., Boeglin M., Poterszman A., Mitschler A., Podjarny A., Rees B., Thierry J. C., Moras D. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science. 1991 Jun 21;252(5013):1682–1689. doi: 10.1126/science.2047877. [DOI] [PubMed] [Google Scholar]
  21. Sixma T. K., Pronk S. E., Kalk K. H., Wartna E. S., van Zanten B. A., Witholt B., Hol W. G. Crystal structure of a cholera toxin-related heat-labile enterotoxin from E. coli. Nature. 1991 May 30;351(6325):371–377. doi: 10.1038/351371a0. [DOI] [PubMed] [Google Scholar]
  22. Sixma T. K., Pronk S. E., Kalk K. H., van Zanten B. A., Berghuis A. M., Hol W. G. Lactose binding to heat-labile enterotoxin revealed by X-ray crystallography. Nature. 1992 Feb 6;355(6360):561–564. doi: 10.1038/355561a0. [DOI] [PubMed] [Google Scholar]
  23. Stein P. E., Boodhoo A., Tyrrell G. J., Brunton J. L., Read R. J. Crystal structure of the cell-binding B oligomer of verotoxin-1 from E. coli. Nature. 1992 Feb 20;355(6362):748–750. doi: 10.1038/355748a0. [DOI] [PubMed] [Google Scholar]
  24. Swaminathan S., Furey W., Pletcher J., Sax M. Crystal structure of staphylococcal enterotoxin B, a superantigen. Nature. 1992 Oct 29;359(6398):801–806. doi: 10.1038/359801a0. [DOI] [PubMed] [Google Scholar]
  25. Tyrrell G. J., Ramotar K., Toye B., Boyd B., Lingwood C. A., Brunton J. L. Alteration of the carbohydrate binding specificity of verotoxins from Gal alpha 1-4Gal to GalNAc beta 1-3Gal alpha 1-4Gal and vice versa by site-directed mutagenesis of the binding subunit. Proc Natl Acad Sci U S A. 1992 Jan 15;89(2):524–528. doi: 10.1073/pnas.89.2.524. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Weber D. J., Gittis A. G., Mullen G. P., Abeygunawardana C., Lattman E. E., Mildvan A. S. NMR docking of a substrate into the X-ray structure of staphylococcal nuclease. Proteins. 1992 Aug;13(4):275–287. doi: 10.1002/prot.340130402. [DOI] [PubMed] [Google Scholar]
  27. Wilmanns M., Hyde C. C., Davies D. R., Kirschner K., Jansonius J. N. Structural conservation in parallel beta/alpha-barrel enzymes that catalyze three sequential reactions in the pathway of tryptophan biosynthesis. Biochemistry. 1991 Sep 24;30(38):9161–9169. doi: 10.1021/bi00102a006. [DOI] [PubMed] [Google Scholar]

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