Do N-terminal nucleophile hydrolases indeed have a single amino acid catalytic center?: Supporting amino acid residues at the active site of penicillin G acylase

FEBS Journal

Volumn 276, Issue 9, 2009, Pages 2589-2598

  Zhiryakova, Diana ^a   Ivanov, Ivaylo ^b   Ilieva, Sonya ^b   Guncheva, Maya ^a   Galunsky, Boris ^c   Stambolieva, Nicolina ^a  

^a INSTITUTE OF ORGANIC CHEMISTRY   (Bulgaria)

^b UNIVERSITY OF SOFIA   (Bulgaria)

^c HAMBURG UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

Catalytic mechanism; Hammett plot; N terminal nucleophile (Ntn) hydrolase; Penicillin G acylase; Quantum mechanical (QM) and molecular mechanical (MM) modeling

Indexed keywords

ALANINE; AMINO ACID; ASPARAGINE; CARBONYL DERIVATIVE; FUNCTIONAL GROUP; GLUTAMINE; HYDROLASE; NUCLEOPHILE; PENICILLIN AMIDASE;

ACYLATION; AMINO TERMINAL SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; ENERGY; ENZYME ACTIVE SITE; ENZYME KINETICS; ENZYME MECHANISM; ESCHERICHIA COLI; HYDROGEN BOND; HYDROLYSIS; MOLECULAR INTERACTION; MOLECULAR MODEL; PRIORITY JOURNAL; QUANTUM MECHANICS;

ALANINE; AMINO ACIDS; CATALYSIS; ESCHERICHIA COLI; GLUTAMINE; HYDROGEN BONDING; HYDROLASES; HYDROLYSIS; KINETICS; MODELS, MOLECULAR; PENICILLIN AMIDASE; SUBSTRATE SPECIFICITY;

ESCHERICHIA COLI;

EID: 64149120134     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2009.06987.x     Document Type: Article

References (32)

1. Brannigan JA, Dodson G, Duggleby HJ, Moody PCE, Smith JL, Tomchick DR Murzin AG (1995) A protein catalytic framework with an N-terminal nucleophile is capable of self-activation. Nature 378, 416 419.
2. Dodson GG (2000) Catalysis in penicillin G amidase - a member of the Ntn (N terminal nucleophile) hydrolase family. Croatica Chim Acta 73, 901 908.
3. Perakyla M Kollman PA (1997) A simulation of the catalytic mechanism of aspartylglucosaminidase using ab initio quantum mechanics and molecular dynamics. J Am Chem Soc 119, 1189 1196.
4. Liu Y, Guan C Aronson NN (1998) Site-directed mutagenesis of essential residues involved in the mechanism of bacterial glycosylasparaginase. J Biol Chem 273, 9688 9694.
5. Oinonen C Rouvinen J (2000) Structural comparison of Ntn-hydrolases. Prot Sci 9, 2329 2337.
6. Arroyo M, de la Mata I, Acebal C Castillon MP (2003) Biotechnological applications of penicillin acylases: state-of-the-art. Appl Microbiol Biotechnol 60, 507 514.
7. Schoemaker HE, Boesten WHJ, Broxterman QB, Roos EC, Kaptein B van den Tweel WJJ (1997) Application of enzymes in industrial organic synthesis. Chimia 51, 308 310.
8. Kadereit D Waldmann H (2001) Enzymatic protecting group techniques. Chem Rev 101, 3367 3396.
9. Waldmann H Sebastian D (1994) Enzymatic protecting group techniques. Chem Rev 94, 911 937.
10. Duggleby HJ, Tolley SP, Hill CP, Dodson EJ, Dodson G Moody PCE (1995) Penicillin acylase has a single-amino-acid catalytic centre. Nature 373, 264 268.
11. McVey CE, Walsh MA, Dodson GG, Wilson KS Brannigan JA (2001) Crystal structures of penicillin acylase enzyme-substrate complexes: structural insights into the catalytic mechanism. J Mol Biol 313, 139 150.
12. Alkema WB, Hensgens CM, Kroezinga EH, de Vries E, Floris R, van der Laan J-M, Dijkstra BW Janssen DB (2000) Characterization of the β-lactam binding site of penicillin acylase from Escherichia coli by structural and site-directed mutagenesis studies. Prot Eng 13, 857 863.
13. Margolin AL, Svedas VK Berezin IV (1980) Substrate specificity of penicillin amidase from E. coli. Biochim Biophys Acta 616, 283 289.
14. Cole M (1969) Hydrolysis of penicillins and related compounds by the cell-bound penicillin acylase of Escherichia coli. Biochem J 115, 733 739.
15. Guncheva M, Ivanov I, Galunsky B, Stambolieva N Kaneti J (2004) Kinetic studies and molecular modelling attribute a crucial role in the specificity and stereoselectivity of penicillin acylase to the pair ArgA145-ArgB263. Eur J Biochem 271, 2272 2279.
16. Menard A, Castonguay R, Lherbet C, Rivard C, Roupioz Y Keillor JW (2001) Nonlinear free energy relationship in the general-acid-catalyzed acylation of rat kidney γ-glutamyl transpeptidase by a series of γ-glutamyl anilide substrate analogues. Biochemistry 40, 12678 12685.
17. 4-(4′-substituted phenyl)-L- asparagines. Org Biomol Chem 1, 1900 1905.
18. Alkema WB, de Vries E, Floris R Janssen DB (2003) Kinetics of enzyme acylation and deacylation in the penicillin acylase-catalyzed synthesis of β-lactam antibiotics. Eur J Biochem 270, 3675 3683.
19. Galabov B, Cheshmedzhieva D, Ilieva S Hadjieva B (2004) Computational study of the reactivity of N-phenylacetamides in the alkaline hydrolysis reaction. J Phys Chem A 108, 11457 11462.
20. Chilov GG, Sidorova AV Svedas VK (2007) Quantum chemical studies of the catalytic mechanism of N-terminal nucleophile hydrolase. Biochemistry 72, 495 500.
21. 4-(2-acetamido-2-deoxy-β-D- glucopyranosyl)-L-asparagine. Arch Biochem Biophys 391, 165 170.
22. Okada T, Suzuki H, Wada K, Kumagai H Fukuyama K (2006) Crystal structures of gamma-glutamyltranspeptidase from Escherichia coli, a key enzyme in glutathione metabolism, and its reaction intermediate. Proc Natl Acad Sci USA 103, 6471 6476.
23. Oinonen C, Tikkanen R, Rouvinen J Peltonen L (1995) Three-dimensional structure of human lysosomal aspartylglucosaminidase. Nat Struct Biol 2, 1102 1108.
24. Svedas VK, Margolin AL, Sherestyuk CF, Klyosov AA Berezin IV (1977) Phenylmethanesulfonylfluoride inactivation of soluble and immobilized penicillin amidase from E. coli. Kinetic analysis and titration of active site. Bioorg Khim 3, 547 553.
25. Yamagami C, Takao N, Tanaka M, Horisaka K, Asada S Fujita T (1984) A quantitative structure-activity study of anticonvulsant phenylacetanilides. Chem Pharm Bull 32, 5003 5009.
26. Birnbaum LS Powell G (1945) Amines related to epinephrine. III. Amines of the eprocaine type. J Am Chem Soc 67, 1464 1466.
27. Mayo SL, Olafson BD Goddard WA (1990) DREIDING: a generic force field for molecular simulations. J Phys Chem 94, 8897 8909.
28. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA, Stratmann RE, Burant JC et al. (1998) Gaussian 98 (Revision A.7). Gaussian, Inc., Pittsburgh, PA.
29. Peng C, Ayala PY, Schlegel HB Frisch MJ (1996) Using redundant internal coordinates to optimize equilibrium geometries and transition states. J Comp Chem 17, 49 56.
30. Peng C Schlegel HB (1994) Combining synchronous transit and quasi-newton methods for finding transition states. Israeli J Chem 33, 449 454.
31. Corwin H, Leo A Taft RW (1991) A survey of Hammet substituent constants and resonance and field parameters. Chem Rev 91, 165 195.
32. Koppel I, Koppel J, Maria P-C, Gal J-F, Notario R, Vlasov VM Taft RW (1998) Comparison of Brønsted acidities of neutral NH-acids in gas phase, dimethyl sulfoxide and water. Int J Mass Spectrom Ion Processes 175, 61 69.