Conformational response to ligand binding in Phosphomannomutase2: Insights into inborn glycosylation disorder

Journal of Biological Chemistry

Volumn 289, Issue 50, 2014, Pages 34900-34910

  Andreotti, Giuseppina ^a   De Vaca, Israel Cabeza ^b   Poziello, Angelita ^a,e   Monti, Maria Chiara ^c   Guallar, Victor ^b,d   Cubellis, Maria Vittoria ^e  

^a CNR   (Italy)

^b BARCELONA SUPERCOMPUTING CENTER   (Spain)

^c UNIVERSITY OF SALERNO   (Italy)

^d INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

^e UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; ESTERIFICATION; GENE ENCODING; GLUCOSE; GLYCOSYLATION; LIGANDS; PROTEOLYSIS;

ALL-ATOM SIMULATIONS; BISPHOSPHATES; CONFORMATIONAL RESPONSE; DRUG DISCOVERY; ENERGY ORIENTATION; LIGAND BINDING; STRUCTURAL MODELING; SUBSTRATE-BOUND;

CRYSTAL STRUCTURE;

PHOSPHOMANNOMUTASE; PHOSPHOMANNOMUTASE 2; UNCLASSIFIED DRUG; GLUCOSE 6 PHOSPHATE; GLUCOSE-1,6-BISPHOSPHATE; LIGAND; MUTASE; PEPTIDE HYDROLASE; PHOSPHOMANNOMUTASE 2, HUMAN; PROTEIN BINDING;

ARTICLE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME CONFORMATION; ESCHERICHIA COLI; GENE MUTATION; LEISHMANIA MEXICANA; LIGAND BINDING; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN PURIFICATION; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; THERMOSTABILITY; AMINO ACID SEQUENCE; ANALOGS AND DERIVATIVES; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENETICS; GLYCOSYLATION; HUMAN; INBORN ERROR OF METABOLISM; METABOLISM; MOLECULAR GENETICS; MUTATION; PROTEIN CONFORMATION; PROTEIN UNFOLDING; TEMPERATURE;

LEISHMANIA MEXICANA;

AMINO ACID SEQUENCE; ANIMALS; GLUCOSE-6-PHOSPHATE; GLYCOSYLATION; HUMANS; LIGANDS; METABOLISM, INBORN ERRORS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PEPTIDE HYDROLASES; PHOSPHOTRANSFERASES (PHOSPHOMUTASES); PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN UNFOLDING; PROTEOLYSIS; TEMPERATURE;

EID: 84918564491     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M114.586362     Document Type: Article

References (35)

1. Matthijs, G., Schollen, E., Heykants, L., and Grünewald, S. (1999) Phosphomannomutase deficiency: the molecular basis of the classical Jaeken syndrome (CDGS type Ia). Mol. Genet. Metab. 68, 220-226
2. Stenson, P. D., Mort, M., Ball, E. V., Shaw, K., Phillips, A., and Cooper, D. N. (2014) The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum. Genet. 133, 1-9
3. Schollen, E., Kjaergaard, S., Legius, E., Schwartz, M., and Matthijs, G. (2000) Lack of Hardy-Weinberg equilibrium for the most prevalent PMM2 mutation in CDG-Ia (congenital disorders of glycosylation type Ia). Eur. J. Hum. Genet. 8, 367-371
4. Kjaergaard, S., Skovby, F., and Schwartz, M. (1998) Absence of homozygosity for predominant mutations in PMM2 in Danish patients with carbohydrate-deficient glycoprotein syndrome type 1. Eur. J. Hum. Genet. 6, 331-336
5. Bjursell, C., Wahlström, J., Berg, K., Stibler, H., Kristiansson, B., Matthijs, G., and Martinsson, T. (1998) Detailed mapping of the phosphomannomutase 2 (PMM2) gene and mutation detection enable improved analysis for Scandinavian CDG type I families. Eur. J. Hum. Genet. 6, 603-611
6. Grünewald, S. (2009) The clinical spectrum of phosphomannomutase 2 deficiency (CDG-Ia). Biochim. Biophys. Acta 1792, 827-834
7. Cromphout, K., Vleugels, W., Heykants, L., Schollen, E., Keldermans, L., Sciot, R., D'Hooge, R., De Deyn, P. P., von Figura, K., Hartmann, D., Körner, C., and Matthijs, G. (2006) The normal phenotype of Pmm1- deficient mice suggests that Pmm1 is not essential for normal mouse development. Mol. Cell. Biol. 26, 5621-5635
8. Pirard, M., Achouri, Y., Collet, J. F., Schollen, E., Matthijs, G., and Van Schaftingen, E. (1999) Kinetic properties and tissular distribution of mammalian phosphomannomutase isozymes. Biochem. J. 339, 201-207
9. Silvaggi, N. R., Zhang, C., Lu, Z., Dai, J., Dunaway-Mariano, D., and Allen, K. N. (2006) The x-ray crystal structures of human α-phosphomannomutase 1 reveal the structural basis of congenital disorder of glycosylation type 1a. J. Biol. Chem. 281, 14918-14926
10. Kedzierski, L., Malby, R. L., Smith, B. J., Perugini, M. A., Hodder, A. N., Ilg, T., Colman, P. M., and Handman, E. (2006) Structure of Leishmania mexicana phosphomannomutase highlights similarities with human isoforms. J. Mol. Biol. 363, 215-227
11. Andreotti, G., Pedone, E., Giordano, A., and Cubellis, M. V. (2013) Biochemical phenotype of a common disease-causing mutation and a possible therapeutic approach for the phosphomannomutase 2-associated disorder of glycosylation. Mol. Genet. Genomic Med. 1, 32-44
12. Schneider, A., Thiel, C., Rindermann, J., DeRossi, C., Popovici, D., Hoffmann, G. F., Gröne, H. J., and Körner, C. (2012) Successful prenatal mannose treatment for congenital disorder of glycosylation-Ia in mice. Nat. Med. 18, 71-73
13. Sharma, V., Ichikawa, M., He, P., Scott, D. A., Bravo, Y., Dahl, R., Ng, B. G., Cosford, N. D., and Freeze, H. H. (2011) Phosphomannose isomerase inhibitors improve N-glycosylation in selected phosphomannomutase-deficient fibroblasts. J. Biol. Chem. 286, 39431-39438
14. Vega, A. I., Pérez-Cerdá, C., Desviat, L. R., Matthijs, G., Ugarte, M., and Pérez, B. (2009) Functional analysis of three splicing mutations identified in the PMM2 gene: toward a new therapy for congenital disorder of glycosylation type Ia. Hum. Mutat. 30, 795-803
15. Eklund, E. A., Merbouh, N., Ichikawa, M., Nishikawa, A., Clima, J. M., Dorman, J. A., Norberg, T., and Freeze, H. H. (2005) Hydrophobic Man-1-P derivatives correct abnormal glycosylation in type I congenital disorder of glycosylation fibroblasts. Glycobiology 15, 1084-1093
16. Shan, Y., Kim, E. T., Eastwood, M. P., Dror, R. O., Seeliger, M. A., and Shaw, D. E. (2011) How does a drug molecule find its target binding site? J. Am. Chem. Soc. 133, 9181-9183
17. Takahashi, R., Gil, V. A., and Guallar, V. (2014) Monte Carlo free ligand diffusion with Markov state model analysis and absolute binding free energy calculations. J. Chem. Theory Comput. 10, 282-288
18. Borrelli, K. W., Vitalis, A., Alcantara, R., and Guallar, V. (2005) PELE: protein energy landscape exploration. A novel Monte Carlo based technique. J. Chem. Theory Comput. 1, 1304-1311
19. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-254
20. Schrödinger, LLC (2011) Protein Preparation Wizard, Epik version 2.2, Impact version 5.7, Prime version 3.0, Schrödinger, LLC, New York
21. Kaminski, G. A., and Friesner, R. A. (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 105, 6474-6487
22. Onufriev, A., Bashford, D., and Case, D. A. (2004) Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55, 383-394
23. Mizuguchi, K., Deane, C. M., Blundell, T. L., Johnson, M. S., and Overington, J. P. (1998) JOY: protein sequence-structure representation and analysis. Bioinformatics 14, 617-623
24. Connolly, M. L. (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science 221, 709-713
25. Cubellis, M. V., Cailliez, F., and Lovell, S. C. (2005) Secondary structure assignment that accurately reflects physical and evolutionary characteristics. BMC Bioinformatics 6, Suppl. 4, S8
26. Cammisa, M., Correra, A., Andreotti, G., and Cubellis, M. V. (2013) Identification and analysis of conserved pockets on protein surfaces. BMC Bioinformatics 14, Suppl. 7, S9
27. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612
28. Cubellis, M. V., Caillez, F., Blundell, T. L., and Lovell, S. C. (2005) Properties of polyproline II, a secondary structure element implicated in proteinprotein interactions. Proteins 58, 880-892
29. Nogly, P., Matias, P. M., de Rosa, M., Castro, R., Santos, H., Neves, A. R., and Archer, M. (2013) High-resolution structure of an atypical α-phosphoglucomutase related to eukaryotic phosphomannomutases. Acta Crystallogr. D Biol. Crystallogr. 69, 2008-2016
30. Patthy, L., and Smith, E. L. (1975) Identification of functional arginine residues in ribonuclease A and lysozyme. J. Biol. Chem. 250, 565-569
31. Leidenheimer, N. J., and Ryder, K. G. (2014) Pharmacological chaperoning: a primer on mechanism and pharmacology. Pharmacol. Res. 83, 10-19
32. Andreotti, G., Guarracino, M. R., Cammisa, M., Correra, A., and Cubellis, M. V. (2010) Prediction of the responsiveness to pharmacological chaperones: lysosomal human α-galactosidase, a case of study. Orphanet. J. Rare Dis. 5, 36
33. Vermeer, S., Kremer, H. P., Leijten, Q. H., Scheffer, H., Matthijs, G., Wevers, R. A., Knoers, N. A., Morava, E., and Lefeber, D. J. (2007) Cerebellar ataxia and congenital disorder of glycosylation Ia (CDG-Ia) with normal routine CDG screening. J. Neurol. 254, 1356-1358
34. Briones, P., Vilaseca, M. A., Schollen, E., Ferrer, I., Maties, M., Busquets, C., Artuch, R., Gort, L., Marco, M., van Schaftingen, E., Matthijs, G., Jaeken, J., and Chabás, A. (2002) Biochemical and molecular studies in 26 Spanish patients with congenital disorder of glycosylation type Ia. J. Inherit. Metab. Dis. 25, 635-646
35. Le Bizec, C., Vuillaumier-Barrot, S., Barnier, A., Dupre, T., Durand, G., and Seta, N. (2005) A new insight into PMM2 mutations in the French population. Hum. Mutat. 25, 504-505