Insight into the mechanism of aminomutase reaction: A case study of phenylalanine aminomutase by computational approach

Journal of Molecular Graphics and Modelling

Volumn 46, Issue , 2013, Pages 65-73

  Wang, Kang ^a   Hou, Qianqian ^a   Liu, Yongjun ^a,b  

^a SHANDONG UNIVERSITY   (China)

^b NORTHWEST INSTITUTE OF PLATEAU BIOLOGY   (China)

Author keywords

Aminomutase; Density functional calculations; Enzymatic reaction mechanisms; Phenylalanine aminomutase; Stereochemistry

Indexed keywords

AMMONIA; DENSITY FUNCTIONAL THEORY; ENZYMES; ISOMERS; STEREOCHEMISTRY; STEREOSELECTIVITY;

AMINOMUTASE; CALCULATION RESULTS; COMPUTATIONAL APPROACH; DENSITY-FUNCTIONAL METHODS; ENZYMATIC REACTION; PHENYLALANINE AMINOMUTASE; PLAUSIBLE MECHANISMS; REACTION MECHANISM;

AMINO ACIDS;

MUTASE; PHENYLALANINE; PHENYLALANINE AMINOMUTASE; UNCLASSIFIED DRUG;

ARTICLE; CALCULATION; DENSITY FUNCTIONAL THEORY; ENZYME MECHANISM; ENZYME STRUCTURE; ISOMERIZATION; NONHUMAN; PRIORITY JOURNAL; REACTION ANALYSIS; STEREOCHEMISTRY; TAXUS; TAXUS CANADENSIS;

TAXUS CANADENSIS;

AMINOMUTASE; DENSITY FUNCTIONAL CALCULATIONS; ENZYMATIC REACTION MECHANISMS; PHENYLALANINE AMINOMUTASE; STEREOCHEMISTRY;

AMMONIA; CATALYTIC DOMAIN; COMPUTER SIMULATION; INTRAMOLECULAR TRANSFERASES; ISOMERISM; MODELS, MOLECULAR; PHENYLALANINE; PLANT PROTEINS; QUANTUM THEORY; TAXUS;

EID: 84885706575     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2013.09.010     Document Type: Article

References (60)

1. J.M. Poston Leucine 2,3-aminomutase, an enzyme of leucine catabolism J. Biol. Chem. 251 1976 1859 1863
2. T.P. Chirpich, V. Zappia, R.N. Costilow, and H.A. Barker Lysine 2,3-aminomutase. Purification and properties of a pyridoxal phosphate and S-adenosylmethionine-activated enzyme J. Biol. Chem. 245 1970 1778 1789
3. P.C. Prabhakaran, N.-T. Woo, P.S. Yorgey, and S.J. Gould Biosynthesis of blasticidin s from l-a-arginine. Stereochemistry in the arginine-2, 3-aminomutase reaction J. Am. Chem. Soc. 110 1988 5785 5791
4. D.L. Steer, R.A. Lew, P. Perlmutter, A.I. Smith, and M.I. Aguilar Beta-amino acids: versatile peptidomimetics Curr. Med. Chem. 9 2002 811 822
5. G. Lelais, and D. Seebach Beta2-amino acids-syntheses, occurrence in natural products, and components of beta-peptides1,2 Biopolymers 76 2004 206 243 (Pubitemid 38724851)
6. D. Seebach, M. Overhand, F.N.M. Kuhnle, B. Martinoni, L. Oberer, U. Hommel, and H. Widmer β-Peptides: synthesis by Arndt-Eistert homologation with concomitant peptide coupling. Structure determination by NMR and CD spectroscopy and by X-ray crystallography. Helical secondary structure of a β-hexapeptide in solution and its stability towards pepsin Helv. Chim. Acta 79 1996 913 941
7. M. Liu, and M.P. Sibi Temperature dependent reversal of stereochemistry in enantioselective conjugate amine additions Tetrahedron 58 2002 7991 8035
8. D. Pena, A.J. Minnaard, J.G. de Vries, and B.L. Feringa Highly enantioselective rhodium-catalyzed hydrogenation of beta-dehydroamino acid derivatives using monodentate phosphoramidites J. Am. Chem. Soc. 124 2002 14552 14553 (Pubitemid 35425025)
9. A. Duursma, A.J. Minnaard, and B.L. Feringa Highly enantioselective conjugate addition of dialkylzinc reagents to acyclic nitroalkenes: a catalytic route to 2-amino acids, aldehydes, and alcohols J. Am. Chem. Soc. 125 2003 3700 3701 (Pubitemid 36512349)
10. 2hLys, pyrrolidine-3-carboxylic acid) by using DIOZ as chiral auxiliary Helv. Chim. Acta 88 2005 2235 2249 (Pubitemid 41232842)
11. W. Liu, S.D. Christenson, S. Standage, and B. Shen Biosynthesis of the enediyne antitumor antibiotic C-1027 Science 297 2002 1170 1173 (Pubitemid 36193350)
12. X. Yin, T. O'Hare, S.J. Gould, and T.M. Zabriskie Identification and cloning of genes encoding viomycin biosynthesis from Streptomyces vinaceus and evidence for involvement of a rare oxygenase Gene 312 2003 215 224 (Pubitemid 37345127)
13. K. Walker, and R. Croteau Taxol biosynthetic genes Phytochemistry 58 2001 1 7
14. D.J. Aberhart, and J.A. Cotting Mechanistic studies on lysine 2,3-aminomutase: carbon-13-deuterium crossover experiments J. Chem. Soc. Perkin Trans. 1 1988 2119 2122
15. D.J. Aberhart, S.J. Gould, H.J. Lin, T.K. Thiruvengadam, and B.H. Weiller Stereochemistry of lysine 2,3-aminomutase isolated from Clostridium subterminale strain SB4 J. Am. Chem. Soc. 105 1983 5461 5470
16. R.J. Parry, and Z. Kurylo-Borowska Biosynthesis of amino acids. Investigation of the mechanism of beta-tyrosine formation J. Am. Chem. Soc. 102 1980 836 837
17. S.D. Christenson, W. Liu, M.D. Toney, and B. Shen A novel 4-methylideneimidazole-5-one-containing tyrosine aminomutase in enediyne antitumor antibiotic C-1027 biosynthesis J. Am. Chem. Soc. 125 2003 6062 6063 (Pubitemid 36582970)
18. J. Rétey, F. Kunz, D. Arigoni, and T.C. Stadtman Zur kenntnis der beta-lysin-mutase-reaktion: mechanismus und sterischer verlauf Helv. Chim. Acta 61 1978 2989 2998
19. H.P. Chen, S.H. Wu, Y.L. Lin, C.M. Chen, and S.S. Tsay Cloning, sequencing, heterologous expression, purification, and characterization of adenosylcobalamin-dependent d-ornithine aminomutase from Clostridium sticklandii J. Biol. Chem. 276 2001 44744 44750
20. N.A. Magarvey, P.D. Fortin, P.M. Thomas, N.L. Kelleher, and C.T. Walsh Gatekeeping versus promiscuity in the early stages of the andrimid biosynthetic assembly line ACS Chem. Biol. 3 2008 542 554
21. L. Feng, U. Wanninayake, S. Strom, J. Geiger, and K.D. Walker Mechanistic, mutational, and structural evaluation of a taxus phenylalanine aminomutase Biochemistry 50 2011 2919 2930
22. N.D. Ratnayake, U. Wanninayake, J.H. Geiger, and K.D. Walker Stereochemistry and mechanism of a microbial phenylalanine aminomutase J. Am. Chem. Soc. 133 2011 8531 8533
23. D. Röther, L. Poppe, S. Viergutz, B. Langer, and J. Rétey Characterization of the active site of histidine ammonia-lyase from Pseudomonas putida Eur. J. Biochem. 268 2001 6011 6019 (Pubitemid 33132022)
24. Y. Asano, Y. Kato, C. Levy, P. Baker, and D. Rice Structure and function of amino acid ammonia-lyases Biocatal. Biotransform. 22 2004 133 140
25. M. Rettig, A. Sigrist, and J. Rétey Mimicking the reaction of phenylalanine ammonia lyase by a synthetic model Helv. Chim. Acta 83 2000 2246 2265
26. W. Szymanski, B. Wu, B. Weiner, S. de Wildeman, B.L. Feringa, and D.B. Janssen Phenylalanine aminomutase-catalyzed addition of ammonia to substituted cinnamic acids: a route to enantiopure alpha- and beta-amino acids J. Org. Chem. 74 2009 9152 9157
27. T.F. Schwede, J. Retey, and G.E. Schulz Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile Biochemistry 38 1999 5355 5361
28. K.D. Walker, K. Klettke, T. Akiyama, and R.J. Croteau Cloning, Heterologous expression, and characterization of a phenylalanine aminomutase involved in taxol biosynthesis Biol. Chem. 279 2004 53947 53954 (Pubitemid 40053125)
29. J.C. Calabrese, D.B. Jordan, A. Boodhoo, S. Sariaslani, and T. Vannelli Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis Biochemistry 43 2004 11403 11416 (Pubitemid 39186962)
30. S. Rachid, D. Krug, K.J. Weissman, and R. Muller Biosynthesis of (R)-beta-tyrosine and its incorporation into the highly cytotoxic chondramides produced by Chondromyces crocatus J. Biol. Chem. 282 2007 21810 21817 (Pubitemid 47195747)
31. D. Krug, and R. Muller Discovery of additional members of the tyrosine aminomutase enzyme family and the mutational analysis of CmdF ChemBioChem. 10 2009 741 750
32. S.G. Van Lanen, T.J. Oh, W. Liu, E. Wendt-Pienkowski, and B. Shen Characterization of the maduropeptin biosynthetic gene cluster from Actinomadura madurae ATCC 39144 supporting a unifying paradigm for enediyne biosynthesis J. Am. Chem. Soc. 129 2007 13082 13094 (Pubitemid 350058349)
33. C.V. Christianson, T.J. Montavon, G.M. Festin, H.A. Cooke, B. Shen, and S.D. Bruner The mechanism of MIO-based aminomutases in beta-amino acid biosynthesis J. Am. Chem. Soc. 129 2007 15744
34. S. Pilbák, Ö. Farkas, and L. Poppe Mechanism of the tyrosine ammonia lyase reaction-tandem nucleophilic and electrophilic enhancement by a proton transfer Chem. Eur. J. 18 2012 7793 7802
35. S. Bartsch, and U.T. Bornscheuer A single residue influences the reaction mechanism of ammonia lyases and mutases Angew. Chem. Int. Ed. 48 2009 3362 3365
36. O. Amata, T. Marino, N. Russo, and M. Toscano A proposal for mitochondrial processing peptidase catalytic mechanism J. Am. Chem. Soc. 133 2011 17824 17831
37. M.A. Khan, R. Lo, T. Bandyopadhyay, and B. Ganguly Probing the reactivation process of sarin-inhibited acetylcholinesterase with α-nucleophiles: hydroxylamine anion is predicted to be a better antidote with DFT calculations J. Mol. Graphics Modell. 29 2011 1039 1046
38. X. Sheng, Y.J. Liu, and C.B. Liu Theoretical studies on the common catalytic mechanism of transketolase by using simplified models J. Mol. Graphics Modell. 39 2013 23 28
39. S.L. Chen, W.H. Fang, and F. Himo Theoretical study of the phosphotriesterase reaction mechanism J. Phys. Chem. B 111 2007 1253 1255 (Pubitemid 46339049)
40. E.F. Oliveira, N.M.F.S.A. Cerqueira, P.A. Fernandes, and M.J. Ramos Mechanism of formation of the internal aldimine in pyridoxal 5′-phosphate dependent enzymes J. Am. Chem. Soc. 133 2011 15496 15505
41. H.M. Senn, and W. Thiel QM/MM methods for biomolecular systems Angew. Chem. Int. Ed. 48 2009 1198 1229
42. P. Hu, and Y.K. Zhang Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9. An ab initio QM/MM-FE study with multiple initial structures J. Am. Chem. Soc. 128 2006 1272 1278 (Pubitemid 43190640)
43. Q.Q. Hou, L.K. Du, J. Gao, Y.J. Liu, and C.B. Liu QM/MM study on the reaction mechanism of O6-alkylguanine-DNA alkyltransferase J. Phys. Chem. B 114 2010 15296 15300
44. C. Lee, W. Yang, and R.G. Parr Development of the colle-salvetti of the electron density Phys. Rev. B: Condens. Matter 37 1988 785 789
45. A.D. Becke Density-functional exchange-energy approximation with correct asymptotic behavior Phys. Rev. A 38 1988 3098 3100
46. A.D. Becke Density-functional thermochemistry I. The effect of the exchange-only gradient correction J. Chem. Phys. 96 1992 2155 2160
47. A.D. Becke Density-functional thermochemistry. II. The effect of the Perdew-Wang generalized-gradient correlation correction J. Chem. Phys. 97 1992 9173 9177
48. A.D. Becke Density-functional thermochemistry. III. The role of exact exchange J. Chem. Phys. 98 1993 5648 5652
49. M. Frisch GAUSSIAN 03 Revision D. 01 2004 Gaussian Inc. Wallingford, CT
50. S. Miertuš, E. Scrocco, and J. Tomasi Electrostatic interaction of a solute with a continuum. A direct utilizaion of ab initio molecular potentials for the prevision of solvent effects Chem. Phys. 55 1981 117 129
51. R. Cammi, and J. Tomasi The GEPOL-GB method for cavity construction J. Comput. Chem. 16 1995 1449 1458
52. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, and A.J. Olson Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J. Comput. Chem. 19 1998 1639 1662 (Pubitemid 128590223)
53. R. Stowasser, and R. Hoffmann What do the Kohn-Sham orbitals and eigenvalues mean? J. Am. Chem. Soc. 121 1999 3414 3420 (Pubitemid 29190907)
54. F.M. Bickelhaupt, E.J. Baerends, and W. Ravenek Model systems for initial stages of oxidative-addition reactions. Theoretical investigation of η1 and η2 coordination of F2 and H2 to PtCl42- and Cr(CO)5 Inorg. Chem. 29 1990 350 354
55. W. Mutatu, K.L. Klettke, C. Foster, and K.D. Walker Unusual mechanism for an aminomutase rearrangement: retention of configuration at the migration termini Biochemistry 46 2007 9785 9794 (Pubitemid 47328585)
56. B. Wu, W. Szymański, G.G. Wybenga, M.M. Heberling, S. Bartsch, S. de Wildeman, G.J. Poelarends, B.L. Feringa, B.W. Dijkstra, and D.B. Janssen Mechanism-inspired engineering of phenylalanine aminomutase for enhanced β-regioselective asymmetric amination of cinnamates Angew. Chem. Int. Ed. 51 2012 482 486
57. L. Melander, and W.H. Saunders Jr. Reaction Rates of Isotopic Molecules 1987 R.E. Krieger Malabar, FL Chapter 2
58. M.J. Knapp, K. Rickert, and J.P. Klinman Nature of hydrogen transfer in soybean lipoxygenase 1: separation of primary and secondary isotope effects J. Am. Chem. Soc. 124 2002 12218 12228
59. J. Mavri, H. Liu, M.H.M. Olsson, and A. Warshel Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase J. Phys. Chem. B 112 2008 5950 5954
60. S.C.L. Kamerlin, J. Mavri, and A. Warshel Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues FEBS Lett. 584 2010 2759 2766