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Crystal structures of HINT demonstrate that histidine triad proteins are GalT-related nucleotide-binding proteins

Abstract

Histidine triad nucleotide-binding protein (HINT), a dimeric purine nucleotide-binding protein from rabbit heart, is a member of the HIT (histidine triad) superfamily which includes HINT homologues and FHIT (HIT protein encoded at the chromosome 3 fragile site) homologues. Crystal structures of HINT-nucleotide complexes demonstrate that the most conserved residues in the superfamily mediate nucleotide binding and that the HIT motif forms part of the phosphate binding loop. Galactose-1-phosphate uridylyltransferase, whose deficiency causes galactosemia, contains tandem HINT domains with the same fold and mode of nucleotide binding as HINT despite having no overall sequence similarity. Features of FHIT, a diadenosine polyphosphate hydrolase and candidate tumour suppressor, are predicted from HINT-nucleotide structures.

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References

  1. Seraphin, B. The HIT protein family: a new family of proteins present in prokaryotes yeast and mammals. DNA Sequence 3, 177–179 (1992).

    Article  CAS  Google Scholar 

  2. Mozier, N.M., Walsh, M.P. & Pearson, J.D. Characterization of a novel zinc binding site of protein kinase C inhbitor-1. FEBS Lett. 279, 14–18 (1991).

    Article  CAS  Google Scholar 

  3. McDonald, J.R. & Walsh, M.P. Ca2+-binding proteins from bovine brain including a potent inhibitor of protein kinase C. Biochem. J. 232, 559–567 (1985).

    Article  CAS  Google Scholar 

  4. Brzoska, P.M. et al. The product of the ataxia-telangiectasia group d complementing gene, atdc interacts with a protein kinase c substrate and inhibitor. Proc. Natl. Acad. Sci. USA 92, 7824–7828 (1995).

    Article  CAS  Google Scholar 

  5. Lima, C., Klein, M.G., Weinstein, I.B. & Hendrickson, W.A. Three-dimensional structure of human protein kinase C interacting protein 1, a member of the HIT family of proteins. Proc. Natl. Acad. Sci. USA 93, 5357–5362 (1996).

    Article  CAS  Google Scholar 

  6. Brzoska, P.M. et al. Cloning, mapping, and in vivo localization of a human member of the PKCI-1 protein family (PRKCNH1). Genomics 36, 151–156 (1996).

    Article  CAS  Google Scholar 

  7. Simpson, G.G., Clark, G. & Brown, J.W. Isolation of a maize cDNA encoding a protein with extensive similarity to an inhibitor of protein kinase C and a cyanobacterial open reading frame. Biochim. Biophys. Acta 1222, 306–308 (1994).

    Article  CAS  Google Scholar 

  8. Wilson, R. et al. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature 368, 32–38 (1994).

    Article  CAS  Google Scholar 

  9. Frohlich, K.U. et al. Yeast cell cycle protein CDC48p shows full-length homology to the mammalian protein VCP and is a member of a protein family involved in secretion, peroxisome formation, and gene expression. J. Cell Biol. 114, 443–453 (1991).

    Article  CAS  Google Scholar 

  10. Bustos, S.A., Schaefer, M.R. & Golden, S.S. Different and rapid responses of four cyanobacterial psbA transcripts to changes in light intensity. J. Bacteriol. 172, 1998–2004 (1990).

    Article  CAS  Google Scholar 

  11. Fleischmann, R.D. et al. Whole–genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512 (1995).

    Article  CAS  Google Scholar 

  12. Fani, R. et al. Cloning of histidine genes of Azospirillum brasilense: organization of the ABFH gene cluster and nucleotide sequence of the hisB gene. Mol. Gen. Genet. 216, 224–229 (1989).

    Article  CAS  Google Scholar 

  13. Bult, C.J. et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273, 1058–1073 (1996).

    Article  CAS  Google Scholar 

  14. Fraser, C.M. et al. The minimal gene complement of Mycoplasma genitalium. Science 270, 397–403 (1995).

    Article  CAS  Google Scholar 

  15. Ohta, M. et al. The FHIT gene, spanning the chromosome 3p14.2 fragile site and renal carcinoma-associated t(3;8) breakpoint, is abnormal in digestive tract cancers. Cell 84, 587–597 (1996).

    Article  CAS  Google Scholar 

  16. Huang, Y., Garrison, P.N. & Barnes, L.D. Cloning of the Schizosaccharomyces pombe gene encoding diadenosine 5′,5-P1,P4-tetraphosphate (Ap4A) asymmetrical hydrolase: sequence similarity with the histidine triad (HIT) protein family. Biochem. J. 312, 925–932 (1995).

    Article  CAS  Google Scholar 

  17. Barnes, L.D. et al. FHIT, a putative tumor suppressor in humans, is a dinucleoside 5′,5‴-P-1,P-3-triphosphate hydrolase. Biochemistry 35, 11529–11535 (1996).

    Article  CAS  Google Scholar 

  18. McLennan, A.G. Ap4A and Other Dinucleoside Polyphosphatases. (CRC Press, Boca Raton, Florida, 1992).

  19. Sozzi, G. et al The FHIT gene at 3p14.2 is abnormal in lung cancer. Cell 85, 17–26 (1996).

    Article  CAS  Google Scholar 

  20. Sozzi, G. et al. Aberrant FHIT transcripts in Merkel cell carcinoma. Cancer Research 56, 2472–2474 (1996).

    CAS  PubMed  Google Scholar 

  21. Negrini, M. et al. The FHIT gene at 3p14.2 is abnormal in breast carcinomas. Cancer Research 56, 3173–3179 (1996).

    CAS  PubMed  Google Scholar 

  22. Virgilio, L. et al. FHIT gene alterations in head and neck squamous cell carcinomas. Proc. Natl. Acad. Sci. USA 93, 9770–9775 (1996).

    Article  CAS  Google Scholar 

  23. Shridhar, R. et al. Frequent breakpoints in the 3p14.2 fragile site, Fra3b, in pancreatic tumors. Cancer Research 56, 4347–4350 (1996).

    CAS  PubMed  Google Scholar 

  24. Panagopoulos, I. et al. The FHIT and PTPRG genes are deleted in benign proliferative breast disease associated with familial breast cancer and cytogenetic rearrangements of chromosome band 3p14. Cancer Research 56, 4871–4875 (1996).

    CAS  PubMed  Google Scholar 

  25. Mao, L., Fan, Y.H., Lotan, R. & Hong, W.K. Frequent abnormalities of fhit, a candidate tumor suppressor gene, in head and neck cancer cell lines. Cancer Research 56, 5128–5131 (1996).

    CAS  PubMed  Google Scholar 

  26. Man, S., Ellis, I.O., Sibbering, M., Blarney, R.W. & Brook, J.D. High levels of allele loss at the FHIT and ATM genes in non–comedo ductal carcinoma in situ and grade I tubular invasive breast cancers. Cancer Research 56, 5484–5489 (1996).

    CAS  PubMed  Google Scholar 

  27. Yanagisawa, K. et al. Molecular analysis of the FHIT gene at 3p14.2 in lung cancer cell lines. Cancer Research 56, 5579–5582 (1996).

    CAS  PubMed  Google Scholar 

  28. Geurts, J.M.W., Schoenmakers, E.F.P.M., Roijer, E., Stenman, G. & Van de Ven, W.J.M. Expression of reciprocal hybrid transcripts of HMGIC and FHIT in a pleomorphic adenoma of the parotid gland. Cancer Research 57, 13–17 (1997).

    CAS  PubMed  Google Scholar 

  29. Wedekind, J.E., Frey, P.A. & Rayment, I. Three-dimensional structure of galactose-1-phosphate uridylyltransferase from Escherichia coli at 1.8 Å resolution. Biochemistry 34, 11049–11061 (1995).

    Article  CAS  Google Scholar 

  30. Levy, H.L. & Hammersen, G. Newborn screening for galactosemia and other galactose metabolic defects. J. Pediatr. 92, 871–877 (1978).

    Article  CAS  Google Scholar 

  31. Branden, C. & Tooze, J. Introduction to Protein Structure (Garland Publishing, New York, 1991).

    Google Scholar 

  32. Rosen, M.K., Michnick, S.W., Karplus, M. & Schreiber, S.L. Proton and nitrogen sequential assignments and secondary structure determination of the human FK506 and rapamycin binding protein. Biochemistry 30, 4774–4789 (1991).

    Article  CAS  Google Scholar 

  33. Michnick, S.W., Rosen, M.K., Wandless, T.J., Karplus, M. & Schreiber, S.L. Solution structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin. Science 252, 836–839 (1991).

    Article  CAS  Google Scholar 

  34. Moore, J.M., Peattie, D.A., Fitzgibbon, M.J. & Thomson, J.A. Solution structure of the major binding protein for the immunosuppressant FK506. Nature 351, 248–250 (1991).

    Article  CAS  Google Scholar 

  35. Wilson, K.P. et al. Comparitive X-ray Structures of the Major Binding Protein for the Immunosuppressant FK506 (Tacrolimus) in Unliganded Form and in Complex with FK506 and Rapamycin. Acta Crystallogr. D 51, 511–521 (1995).

    Article  CAS  Google Scholar 

  36. Clardy, J. The chemistry of signal transduction. Proc. Natl. Acad. Sci. USA 92, 56–61 (1995).

    Article  CAS  Google Scholar 

  37. Guranowski, A. & Sillero, A. Enzymes cleaving dinucleoside polyphosphates. in Ap4A and Other Dinucleoside Polyphosphates (ed. McLennan, A.G.) 81–133 (CRC Press, Boca Raton, FL, 1992).

    Google Scholar 

  38. Booth, J.W. & Guidotti, G. An alleged yeast polyphosphate kinase is actually diadenosine-5′, 5‴-P1,P4-tetraphosphate alpha, beta-phosphorylase. J. Biol. Chem. 270, 19377–19382 (1995).

    Article  CAS  Google Scholar 

  39. Wedekind, J.E., Frey, P.A. & Rayment, I. The structure of nucleotidylated Histidine-166 of Galactose-1-Phosphate Uridylyltransferase provides insight into phosphoryl group transfer. Biochemistry 35, 11560–11569 (1996).

    Article  CAS  Google Scholar 

  40. Robinson, A.K., de la Pena, C.E. & Barnes, L.D. Isolation and characterization of diadenosine tetraphosphate (Ap4A) hydrolase from Schizosaccharomyces pombe. Biochemica et Biophysica Acta 1161, 139–148 (1993).

    Article  CAS  Google Scholar 

  41. Kitzler, J.W., Farr, S.B. & Ames, B.N. Intracellular functions of ApnN: prokaryotes. in Ap4A and Other Dinucleoside Polyphosphates (ed. McLennan, A.G.) (CRC Press, Boca Raton, FL, 1992).

    Google Scholar 

  42. Vartanian, A., Narovlyansky, A., Amchenkova, A., Turpaev, K. & Kisselev, L. Interferons induce accumulation of diadenosine triphosphate (Ap3A) in human cultured cells. FEBS Lett. 381, 32–34 (1996).

    Article  CAS  Google Scholar 

  43. Segal, E. & Le Pecq, J.B. Relationship between cellular diadenosine 5′,5‴-P1,P4-tetraphosphate level, cell density, cell growth stimulation and toxic stresses. Exp. Cell Res. 167, 119–126 (1986).

    Article  CAS  Google Scholar 

  44. Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26, 795–800 (1993).

    Article  CAS  Google Scholar 

  45. Sheldrick, G.M. SHELXS86, a Program for the Solution of Crystal Structures, (Univ. of Gottingen, Gottingen, FRG, 1985).

    Google Scholar 

  46. Ten Eyck, L.F. & Arnone, A. Three-dimensional Fourier Synthesis of Human Deoxyhemoglobin at 2.5 Angstrom Resolution. J. Mol. Biol. 100, 3–11 (1976).

    Article  CAS  Google Scholar 

  47. Wang, B.C. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115, 90–112 (1985).

    Article  CAS  Google Scholar 

  48. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

  49. Kabsch, W., Mannherz, H.G., Suck, D., Pai, E.F. & Holmes, K.C. Atomic structure of the actin:DNAse I complex. Nature 347, 37–44 (1990).

    Article  CAS  Google Scholar 

  50. Brunger, A.T. X-PLOR Version 3.1 Manual (Yale University, New Haven, Connecticut, 1993).

    Google Scholar 

  51. Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. D 50, 157–163 (1994).

    Article  Google Scholar 

  52. Brunger, G.J. The free R value: a more objective statistic for crystallography. Methods in Enzymol. 277, in press (1997).

  53. Barton, G.J. ALSCRIPT, a tool to format multiple sequence alignments. Protein Engineering 6, 37–40 (1993).

    Article  CAS  Google Scholar 

  54. Kraulis, P.J. MolScript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

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Brenner, C., Garrison, P., Gilmour, J. et al. Crystal structures of HINT demonstrate that histidine triad proteins are GalT-related nucleotide-binding proteins. Nat Struct Mol Biol 4, 231–238 (1997). https://doi.org/10.1038/nsb0397-231

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