A theoretical study on the catalytic mechanism of the retaining α-1,2-mannosyltransferase Kre2p/Mnt1p: The impact of different metal ions on catalysis

Organic and Biomolecular Chemistry

Volumn 12, Issue 24, 2014, Pages 4201-4210

  Bobovská, Adela ^a,b   Tvaroška, Igor ^a   Kóňa, Juraj ^a  

^a INSTITUTE OF CHEMISTRY   (Slovakia)

^b Physics and Informatics   (Slovakia)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM; ENZYMES; ISOTOPES; MANGANESE; METAL IONS; QUANTUM CHEMISTRY; SUBSTITUTION REACTIONS; ZINC;

ANOMERIC CONFIGURATION; CATALYTIC MECHANISMS; GLYCOSYLTRANSFERASES; KINETIC ISOTOPE EFFECTS; NUCLEOPHILIC SUBSTITUTION REACTIONS; RATE DETERMINING STEP; STRUCTURAL PARAMETER; THROUGH-SPACE INTERACTION;

CATALYSIS;

ION; KRE2 PROTEIN, S CEREVISIAE; LIGAND; MANNOSYLTRANSFERASE; METAL; SACCHAROMYCES CEREVISIAE PROTEIN;

BIOCATALYSIS; CHEMICAL STRUCTURE; DRUG EFFECTS; ENZYMOLOGY; METABOLISM; QUANTUM THEORY; SACCHAROMYCES CEREVISIAE; THERMODYNAMICS;

BIOCATALYSIS; IONS; LIGANDS; MANNOSYLTRANSFERASES; METALS; MODELS, MOLECULAR; QUANTUM THEORY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; THERMODYNAMICS;

EID: 84901675902     PISSN: 14770520     EISSN: None     Source Type: Journal    
DOI: 10.1039/c4ob00286e     Document Type: Article

References (69)

1. L. L. Lairson B. Henrissat G. J. Davies S. G. Withers Annu. Rev. Biochem. 2008 77 521 555
2. N. Soya Y. Fang M. M. Palcic J. S. Klassen Glycobiology 2011 21 547 552
3. E. A. Eklund, L. Bode and H. H. Freeze, in Comprehensive Glycoscience. From Chemistry to Systems Biology, ed., J. P. Kamerling, G. J. Boons, Y. C. Lee, A. Suzuki, N. Taniguchi, and, A. G. J. Voragen, Elsevier, Oxford, 1st edn, 2007, vol. 4, pp. 339-371
4. R. Zhang, V. L. Y. Yip and S. G. Withers, in Comprehensive Natural products II: Chemistry and Biology, ed., L. Mander, and, H.-W. Liu, Elsevier, 1st edn, 2010, vol. 8, pp. 385-422
5. P. K. Qasba and B. Ramakrishnan, in Comprehensive Glycoscience. From Chemistry to Systems Biology, ed., J. P. Kamerling, G. J. Boons, Y. C. Lee, A. Suzuki, N. Taniguchi, and, A. G. J. Voragen, Elsevier, Oxford, 1st edn, 2007, vol. 2, pp. 251-281
6. I. TvaroŠka Mini-Rev. Org. Chem. 2011 8 263 269
7. I. TvaroŠka Trends Glycosci. Glyc. 2005 17 177 190
8. I. TvaroŠka S. Kozmon M. Wimmerová J. Kóča Chem.-Eur. J. 2013 19 8153 8162
9. I. TvaroŠka S. Kozmon M. Wimmerová J. Kóča J. Am. Chem. Soc. 2012 134 15563 15571
10. C. Breton L. Snajdrová C. Jeanneau J. Kóča A. Imberty Glycobiology 2006 16 29r 37r
11. A. Ardèvol C. Rovira Angew. Chem., Int. Ed. 2011 50 1 6
12. V. Rojas-Cervellera A. Ardèvol M. Boero A. Planas C. Rovira Chem.-Eur. J. 2013 19 14018 14023
13. I. TvaroŠka, in Nmr Spectroscopy and Computer Modeling of Carbohydrates: Recent Advances, ed., J. F. G. Vliegenthart, and, R. J. Woods, ACS Sym. Ser., 2006, vol. 930, pp. 285-301
14. T. Trnka, S. Kozmon, I. TvaroŠka and J. Kóča, PloS Comput. Biol., submitted
15. A. Bobovská, I. TvaroŠka and J. Kóňa, Glycobiology, submitted
16. H. Gómez I. Polyak W. Thiel J. M. Lluch L. Masgrau J. Am. Chem. Soc. 2012 134 4743 4752
17. H. Gómez J. M. Lluch L. Masgrau Carbohydr. Res. 2012 356 204 208
18. H. Gómez J. M. Lluch L. Masgrau J. Am. Chem. Soc. 2013 135 7053 7063
19. Maestro, version 9.2; Schrödinger, LLC, New York, NY, 2011
20. B. Ramakrishnan E. Boeggeman P. K. Qasba Biochemistry 2004 43 12513 12522
21. V. Ramasamy E. E. Boeggeman B. Ramakrishnan D. M. Ratner P. H. Seeberger P. K. Qasba Glycobiology 2004 14 1105 1106
22. C. J. Zea G. Camci-Unal N. L. Pohl Chem. Cent. J. 2008 2 15
23. J. Kóňa I. TvaroŠka Chem. Pap. 2009 63 598 607
24. Y. D. Lobsanov P. A. Romero B. Sleno B. Yu P. Yip A. Herscovics P. L. Howell J. Biol. Chem. 2004 279 17921 17931
25. L. M. Thomson S. Bates S. Yamazaki M. Arisawa Y. Aoki N. A. R. Gow J. Biol. Chem. 2000 275 18933 18938
26. P. K. Qasba B. Ramakrishnan E. Boeggeman Trends Biochem. Sci. 2005 30 53 62
27. E. Boix G. J. Swaminathan Y. N. Zhang R. Natesh K. Brew K. R. Acharya J. Biol. Chem. 2001 276 48608 48614
28. K. Persson H. D. Ly M. Dieckelmann W. W. Wakarchuk S. G. Withers N. C. J. Strynadka Nat. Struct. Biol. 2001 8 166 175
29. W. W. Cleland Adv. Phys. Org. Chem. 2010 44 1 17
30. S. L. Marcus R. Polakowski N. O. Seto E. Leinala S. Borisova A. Blancher F. Roubinet S. V. Evans M. M. Palcic J. Biol. Chem. 2003 278 12403 12405
31. A. Monegal A. Planas J. Am. Chem. Soc. 2006 128 16030 16031
32. S. S. Lee S. Y. Hong J. C. Errey A. Izumi G. J. Davies B. G. Davies Nat. Chem. Biol. 2011 7 631 638
33. T. A. Fritz J. Raman L. A. Tabak J. Biol. Chem. 2006 281 8613 8619
34. S. C. Kim A. N. Singh F. M. Raushel J. Biol. Chem. 1988 263 10151 10154
35. S. C. Kim A. N. Singh F. M. Raushel Arch. Biochem. Biophys. 1988 267 54 59
36. B. W. Murray V. Wittmann M. D. Burkart S. C. Hung C. H. Wong Biochemistry 1997 36 823 831
37. J. Chan A. Tang A. J. Bennet J. Am. Chem. Soc. 2012 134 1212 1220
38. R. M. Werner J. T. Stivers Biochemistry 2000 39 14054 14064
39. Y. Zhang M. K. Luo V. L. Schramm J. Am. Chem. Soc. 2009 131 4685 4694
40. B. J. Lynch D. G. Truhlar J. Phys. Chem. A 2001 105 2936 2941
41. Y. Zhao D. G. Truhlar Theor. Chem. Acc. 2008 120 215 241
42. L. H. Hu P. Soderhjelm U. Ryde J. Chem. Theory Comput. 2011 7 761 777
43. J. L. Fattebert R. J. Law B. Bennion E. Y. Lau E. Schwegler F. C. Lightstone J. Chem. Theory Comput. 2009 5 2257 2264
44. E. Boix Y. N. Zhang G. J. Swaminathan K. Brew K. R. Acharya J. Biol. Chem. 2002 277 28310 28318
45. E. Boeggeman P. K. Qasba Glycobiology 2002 12 395 407
46. M. Lussier A. M. Sdicu T. Ketela H. Bussey J. Cell Biol. 1995 131 913 927
47. M. Lussier A. M. Sdicu F. Bussereau M. Jacquet H. Bussey J. Biol. Chem. 1997 272 15527 15531
48. Desmond, version 3.0; Schrödinger, LLC, New York, NY, 2011
49. Epik version 2.2, Schrödinger, LLC, New York, NY, 2011
50. Impact version 5.7, Schrödinger, LLC, New York, NY, 2011
51. Prime version 3.0, Schrödinger, LLC, New York, NY, 2011
52. D. C. Bas D. M. Rogers J. H. Jensen Proteins 2008 73 765 783
53. H. Li A. D. Robertson J. H. Jensen Proteins 2005 61 704 721
54. Qsite, version 5.7, Schrödinger, LLC, New York, NY, 2011
55. Jaguar, version 7.8, Schrödinger, LLC, New York, NY, 2011
56. Impact, version 5.7, Schrödinger, LLC, New York, NY, 2011
57. W. R. Wadt P. J. Hay J. Chem. Phys. 1985 82 284 298
58. P. J. Hay W. R. Wadt J. Chem. Phys. 1985 82 270 283
59. G. I. Csonka A. D. French G. P. Johnson C. A. Stortz J. Chem. Theory Comput. 2009 5 679 692
60. R. K. Raju A. Ramraj I. H. Hillier M. A. Vincent N. A. Burton Phys. Chem. Chem. Phys. 2009 11 3411 3416
61. A. D. Becke J. Chem. Phys. 1993 98 5648 5652
62. C. T. Lee W. T. Yang R. G. Parr Phys. Rev. B: Condens. Matter 1988 37 785 789
63. G. A. Kaminski R. A. Friesner J. Tirado-Rives W. L. Jorgensen J. Phys. Chem. B 2001 105 6474 6487
64. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren and J. Hermans, in Intermolecular Forces, ed., B. Pullman, Reidel, Dordrecht, The Netherlands, 1st edn, 1981, vol. 11, pp. 331-338
65. J. M. Bofill J. Comput. Chem. 1994 15 1
66. B. A. Murtagh R. W. H. Sargent Comput. J. 1970 13 185
67. M. J. D. Powell Math. Prog. 1971 1 26
68. M. E. Mura P. J. Knowles J. Chem. Phys. 1996 104 9848
69. S. E. Wheeler K. N. Houk J. Chem. Theory Comput. 2010 6 395 404