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Insights into mucopolysaccharidosis I from the structure and action of α-L-iduronidase

Nature Chemical Biology volume 9, pages 739–745 (2013)Cite this article

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An Erratum to this article was published on 18 October 2013

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Abstract

Mucopolysaccharidosis type I (MPS I), caused by mutations in the gene encoding α-L-iduronidase (IDUA), is one of approximately 70 genetic disorders collectively known as the lysosomal storage diseases. To gain insight into the basis for MPS I, we crystallized human IDUA produced in an Arabidopsis thaliana cgl mutant. IDUA consists of a TIM barrel domain containing the catalytic site, a β-sandwich domain and a fibronectin-like domain. Structures of IDUA bound to iduronate analogs illustrate the Michaelis complex and reveal a 2,5B conformation in the glycosyl-enzyme intermediate, which suggest a retaining double displacement reaction involving the nucleophilic Glu299 and the general acid/base Glu182. Unexpectedly, the N-glycan attached to Asn372 interacts with iduronate analogs in the active site and is required for enzymatic activity. Finally, these IDUA structures and biochemical analysis of the disease-relevant P533R mutation have enabled us to correlate the effects of mutations in IDUA to clinical phenotypes.

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Figure 1: Overview of the IDUA molecule and close-up view of the catalytic domain.
Figure 2: Schematic views of the polar interactions between IdoA analogs and IDUA.
Figure 3: The catalytic pathway for human IDUA and supporting crystallographic evidence.
Figure 4: Marked effects of deglycosylation by CBM-PNGase F on the hydrolytic activity of cgl IDUA and kinetic parameters.
Figure 5: Structural and biochemical analyses of the P533R mutation in IDUA.

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  • 20 September 2013

    In the version of this article initially published online, in the Online Methods section 'Synthesized IDUA inhibitors', two different chemical names were provided for 5F-IdoAF, and a complete name for 2F-IdoAF was inadvertently omitted. Additionally, in the legend for Figure 5, one instance of mg−1 was mistakenly written as mg−. The page numbers for reference 6 were also incorrect. These errors have been corrected for the print, PDF and HTML versions of this article.

References

  1. Clarke, L.A. The mucopolysaccharidoses: a success of molecular medicine. Expert Rev. Mol. Med. 10, e1 (2008).

    Article  Google Scholar 

  2. Roubicek, M., Gehler, J. & Spranger, J. The clinical spectrum of α-L-iduronidase deficiency. Am. J. Med. Genet. 20, 471–481 (1985).

    Article  CAS  Google Scholar 

  3. Valenzano, K.J. et al. Identification and characterization of pharmacological chaperones to correct enzyme deficiencies in lysosomal storage disorders. Assay Drug Dev. Technol. 9, 213–235 (2011).

    Article  CAS  Google Scholar 

  4. Tropak, M.B. et al. Identification of pharmacological chaperones for Gaucher disease and characterization of their effects on β-glucocerebrosidase by hydrogen/deuterium exchange mass spectrometry. ChemBioChem 9, 2650–2662 (2008).

    Article  CAS  Google Scholar 

  5. Yu, Z., Sawkar, A.R. & Kelly, J.W. Pharmacologic chaperoning as a strategy to treat Gaucher disease. FEBS J. 274, 4944–4950 (2007).

    Article  CAS  Google Scholar 

  6. Neufeld, E.F. & Muenzer, J. The Metabolic and Molecular Bases of Inherited Disease Vol. III (eds. Scriver, C.R. et al.) 3421–3452 (McGraw-Hill, New York, 2001).

    Google Scholar 

  7. Terlato, N.J. & Cox, G.F. Can mucopolysaccharidosis type I disease severity be predicted based on a patient's genotype? A comprehensive review of the literature. Genet. Med. 5, 286–294 (2003).

    Article  CAS  Google Scholar 

  8. Nieman, C.E. et al. Family 39 α-L-iduronidases and β-D-xylosidases react through similar glycosyl-enzyme intermediates: identification of the human iduronidase nucleophile. Biochemistry 42, 8054–8065 (2003).

    Article  CAS  Google Scholar 

  9. Yang, J.K. et al. Crystal structure of β-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase. J. Mol. Biol. 335, 155–165 (2004).

    Article  CAS  Google Scholar 

  10. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    Article  CAS  Google Scholar 

  11. Rempel, B.P., Clarke, L.A. & Withers, S.G. A homology model for human α-L-iduronidase: insights into human disease. Mol. Genet. Metab. 85, 28–37 (2005).

    Article  CAS  Google Scholar 

  12. Zhao, K.W., Faull, K.F., Kakkis, E.D. & Neufeld, E.F. Carbohydrate structures of recombinant human α-L-iduronidase secreted by Chinese hamster ovary cells. J. Biol. Chem. 272, 22758–22765 (1997).

    Article  CAS  Google Scholar 

  13. He, X. et al. Characterization and downstream mannose phosphorylation of human recombinant α-L-iduronidase produced in Arabidopsis complex glycan-deficient (cgl) seeds. Plant Biotechnol J. 10.1111/pbi.12096 (31 July 2013).

  14. Vocadlo, D.J., MacKenzie, L.F., He, S., Zeikus, G.J. & Withers, S.G. Identification of glu-277 as the catalytic nucleophile of Thermoanaerobacterium saccharolyticum β-xylosidase using electrospray MS. Biochem. J. 335, 449–455 (1998).

    Article  CAS  Google Scholar 

  15. Armand, S. et al. Stereochemical course and reaction products of the action of β-xylosidase from Thermoanaerobacterium saccharolyticum strain B6A-RI. Eur. J. Biochem. 236, 706–713 (1996).

    Article  CAS  Google Scholar 

  16. Rostkowski, M., Olsson, M.H., Sondergaard, C.R. & Jensen, J.H. Graphical analysis of pH-dependent properties of proteins predicted using PROPKA. BMC Struct. Biol. 11, 6 (2011).

    CAS  Google Scholar 

  17. Maita, N. et al. Human α-L-iduronidase uses its own N-glycan as a substrate-binding and catalytic module. Proc. Natl. Acad. Sci. USA 110, 14628–14633 (2013).

    Article  CAS  Google Scholar 

  18. Hopwood, J.J. & Muller, V. Diagnostic enzymology of α-L-iduronidase with special reference to a sulfated disaccharide derived from heparin. Clin. Sci. (Lond.) 62, 193–201 (1982).

    Article  CAS  Google Scholar 

  19. Yogalingam, G. et al. Identification and molecular characterization of α-L-iduronidase mutations present in mucopolysaccharidosis type I patients undergoing enzyme replacement therapy. Hum. Mutat. 24, 199–207 (2004).

    Article  CAS  Google Scholar 

  20. Clements, P.R., Muller, V. & Hopwood, J.J. Human α-L-iduronidase. 2. Catalytic properties. Eur. J. Biochem. 152, 29–34 (1985).

    Article  CAS  Google Scholar 

  21. Vocadlo, D.J., Davies, G.J., Laine, R. & Withers, S.G. Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate. Nature 412, 835–838 (2001).

    Article  CAS  Google Scholar 

  22. Davies, G.J., Planas, A. & Rovira, C. Conformational analyses of the reaction coordinate of glycosidases. Acc. Chem. Res. 45, 308–316 (2012).

    Article  CAS  Google Scholar 

  23. Koshland, D.E. Stereochemistry and the mechanism of enzymatic reactions. Biol. Rev. Camb. Philos. Soc. 28, 416–436 (1953).

    Article  CAS  Google Scholar 

  24. Heightman, T.D. & Vasella, A.T. Recent insights into inhibition, structure, and mechanism of configuration-retaining glycosidases. Angew. Chem. Int. Edn Engl. 38, 750–770 (1999).

    Article  CAS  Google Scholar 

  25. Sabini, E. et al. Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase. Chem. Biol. 6, 483–492 (1999).

    Article  CAS  Google Scholar 

  26. Sidhu, G. et al. Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase. Biochemistry 38, 5346–5354 (1999).

    Article  CAS  Google Scholar 

  27. Matte, U. et al. Identification and characterization of 13 new mutations in mucopolysaccharidosis type I patients. Mol. Genet. Metab. 78, 37–43 (2003).

    Article  CAS  Google Scholar 

  28. Alif, N. et al. Mucopolysaccharidosis type I: characterization of a common mutation that causes Hurler syndrome in Moroccan subjects. Ann. Hum. Genet. 63, 9–16 (1999).

    Article  CAS  Google Scholar 

  29. Laradi, S. et al. Mucopolysaccharidosis I: α-L-iduronidase mutations in three Tunisian families. J. Inherit. Metab. Dis. 28, 1019–1026 (2005).

    Article  CAS  Google Scholar 

  30. Scott, H.S. et al. α-L-Iduronidase mutations (Q70X and P533R) associate with a severe Hurler phenotype. Hum. Mutat. 1, 333–339 (1992).

    Article  CAS  Google Scholar 

  31. Bunge, S. et al. Genotype-phenotype correlations in mucopolysaccharidosis type I using enzyme kinetics, immunoquantification and in vitro turnover studies. Biochim. Biophys. Acta 1407, 249–256 (1998).

    Article  CAS  Google Scholar 

  32. Bashyal, B.P., Chow, H.-F., Fellows, L.E. & Fleet, G.W.J. The synthesis of polyhydroxylated amino acids from glucuronolactone: enantiospecific synthesis of 2S,3R,4R,5S-trihydroxypipecolic acid, 2R,3R,4R,5S-trihydroxypipecolic acid and 2R,3R,4R-dihydroxyproline. Tetrahedron 43, 415–422 (1987).

    Article  CAS  Google Scholar 

  33. Downing, W.L. et al. Synthesis of enzymatically active human α-L-iduronidase in Arabidopsis cgl (complex glycan-deficient) seeds. Plant Biotechnol. J. 4, 169–181 (2006).

    Article  CAS  Google Scholar 

  34. He, X. et al. Production of α-L-iduronidase in maize for the potential treatment of a human lysosomal storage disease. Nat. Commun. 3, 1062 (2012).

    Article  Google Scholar 

  35. He, X. et al. Influence of an ER-retention signal on the N-glycosylation of recombinant human α-L-iduronidase generated in seeds of Arabidopsis. Plant Mol. Biol. 79, 157–169 (2012).

    Article  CAS  Google Scholar 

  36. Ruth, L., Eisenberg, D. & Neufeld, E.F. α-L-iduronidase forms semi-crystalline spherulites with amyloid-like properties. Acta Crystallogr. D Biol. Crystallogr. 56, 524–528 (2000).

    Article  CAS  Google Scholar 

  37. Kabsch, W. Xds. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010).

    Article  CAS  Google Scholar 

  38. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  39. Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    Article  CAS  Google Scholar 

  40. Langer, G., Cohen, S.X., Lamzin, V.S. & Perrakis, A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protoc. 3, 1171–1179 (2008).

    Article  CAS  Google Scholar 

  41. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article  Google Scholar 

  42. Winn, M.D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242 (2011).

    Article  CAS  Google Scholar 

  43. Murshudov, G.N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355–367 (2011).

    Article  CAS  Google Scholar 

  44. Word, J.M., Lovell, S.C., Richardson, J.S. & Richardson, D.C. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285, 1735–1747 (1999).

    Article  CAS  Google Scholar 

  45. McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

    Article  CAS  Google Scholar 

  46. Winn, M.D., Murshudov, G.N. & Papiz, M.Z. Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol. 374, 300–321 (2003).

    Article  CAS  Google Scholar 

  47. Painter, J. & Merritt, E.A. Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr. D Biol. Crystallogr. 62, 439–450 (2006).

    Article  Google Scholar 

  48. Laskowski, R.A., Macarthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–291 (1993).

    Article  CAS  Google Scholar 

  49. Chakrabarty, R. et al. PSITE vectors for stable integration or transient expression of autofluorescent protein fusions in plants: probing Nicotiana benthamiana–virus interactions. Mol. Plant Microbe Interact. 20, 740–750 (2007).

    Article  CAS  Google Scholar 

  50. Babajani, G., Tropak, M.B., Mahuran, D.J. & Kermode, A.R. Pharmacological chaperones facilitate the post-ER transport of recombinant N370S mutant β-glucocerebrosidase in plant cells: evidence that N370S is a folding mutant. Mol. Genet. Metab. 106, 323–329 (2012).

    Article  CAS  Google Scholar 

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Acknowledgements

This paper is dedicated to the memory of John Colter (1923–2013), chair of the Department of Biochemistry, University of Alberta, from 1961 to 1987. We thank S. Khan for his technical assistance during in-house data collection and the staff at the Canadian Light Source in Saskatoon and the Stanford Synchrotron Radiation Lightsource for their assistance in the data collection. We are grateful for the initial work done by K. Bateman on the growth of the monoclinic form of IDUA crystals, for synthetic work performed by A. Wong and for the expression and purification of CBM-PNGase-F by E. Kwan. We also thank J. Hopwood for the monoclonal antibody to human IDUA. M.N.G.J. and A.R.K. are grateful for the funding support from the Canadian Institutes for Health Research (grant no. MOP123222). H.B. thanks Alberta Innovates Health Solution for the fellowship support. E.D.G.-B. thanks the Canadian Institute of Health Research for a postdoctoral fellowship. A.R.K. is grateful for funding support from the Canadian Society for Mucopolysaccharide and Related Diseases and to the Michael Smith Foundation for Health Research for the Senior Scholar Award (award no. CI-SSH-01915(07-1)).

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Author notes

  1. Haiying Bie, Jiang Yin and Xu He: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada

    Haiying Bie, Jiang Yin & Michael N G James

  2. Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada

    Xu He & Allison R Kermode

  3. Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada

    Ethan D Goddard-Borger & Stephen G Withers

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Contributions

X.H. and A.R.K. performed protein production and purification and the comparative kinetics work related to IDUA deglycosylation and IDUAP533R. E.D.G.-B. performed chemical synthesis and other enzyme kinetics. H.B. crystallized the protein. H.B. and J.Y. collected the diffraction data and carried out structure determination. H.B., J.Y. and M.N.G.J. analyzed the data and wrote the paper with contributions from X.H., A.R.K., S.G.W. and E.D.G.-B. M.N.G.J. and A.R.K. supervised the project.

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Correspondence to Michael N G James.

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Supplementary Results, Supplementary Note, Supplementary Figures 1–3 and Supplementary Tables 1–4. (PDF 479 kb)

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Bie, H., Yin, J., He, X. et al. Insights into mucopolysaccharidosis I from the structure and action of α-L-iduronidase. Nat Chem Biol 9, 739–745 (2013). https://doi.org/10.1038/nchembio.1357

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