A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels

Structure - Tập 7 - Trang 205-216 - 1999
Stefano Benini1, Wojciech R Rypniewski1, Keith S Wilson2, Silvia Miletti3, Stefano Ciurli4, Stefano Mangani5
1European Molecular Biology Laboratory, DESY, Notkestraße 85, D-22603, Hamburg, Germany
2Department of Chemistry, University of York, Heslington, York YO1 5DD, United Kingdom
3Institute of Agricultural Chemistry, University of Bologna, Viale Berti Pichat 10, I-40127, Bologna, Italy
4Institute of Agricultural Chemistry, University of Bologna, Viale Berti Pichat 10, I-40127, Bologna, Italy e-mail: [email protected]
5Department of Chemistry, University of Siena, Pian dei Mantellini, 44 I-53100, Siena, Italy e-mail: [email protected]

Tài liệu tham khảo

Jabri, 1995, The crystal structure of urease from Klebsiella aerogenes, Science, 268, 998, 10.1126/science.7754395 Karplus, 1997, 70 years of crystalline urease: what have we learned?, Acc. Chem. Res, 30, 330, 10.1021/ar960022j Wang, 1994, Structure of the dinuclear active site of urease. X-ray absorption spectroscopic study of native and 2-mercaptoethanol-inhibited bacterial and plant enzymes, Inorg. Chem, 33, 1589, 10.1021/ic00086a006 Blakeley, 1983, Jack bean urease. VII. Light scattering and nickel(II) spectrum. Thiolate-nickel(II) charge transfer peaks in the spectrum of the β-mercaptoethanol-urease complex, Biochim. Biophys. Acta, 744, 219, 10.1016/0167-4838(83)90094-8 Hasnain, 1983, An EXAFS study of jack bean urease, a nickel metalloenzyme, Biochem. Biophys. Res. Commun, 112, 279, 10.1016/0006-291X(83)91827-2 Alagna, 1984, The nickel ion environment in jack bean urease, Biochem. J, 220, 591, 10.1042/bj2200591 Clark, 1989, Magnetic properties of the nickel enzyme urease, nickel-substituted carboxypeptidase A, and nickel-substituted carbonic anhydrase, Inorg. Chem, 28, 1326, 10.1021/ic00306a024 Clark, 1990, X-ray absorption spectroscopic evidence for binding of the competitive inhibitor 2-mercaptoethanol to the nickel sites of jack bean urease. A new Ni-Ni interaction in the inhibited enzyme, Inorg. Chem, 29, 579, 10.1021/ic00329a002 Finnegan, 1991, Variable temperature magnetic circular dichroism spectroscopy as a probe of the electronic and magnetic properties of nickel in jack bean urease, J. Am. Chem. Soc, 113, 4030, 10.1021/ja00010a076 Benini, 1996, X-ray absorption spectroscopy study of native and phenylphosphorodiamidate-inhibited Bacillus pasteurii urease, Eur. J. Biochem, 239, 61, 10.1111/j.1432-1033.1996.0061u.x Zerner, 1991, Recent advances in the chemistry of an old enzyme, urease, Bioorg. Chem, 19, 116, 10.1016/0045-2068(91)90048-T Pearson, 1997, Structures of Cys319 variants and acetohydroxamate-inhibited Klebsiella aerogenes urease, Biochemistry, 36, 8164, 10.1021/bi970514j Benini, 1996, Bacillus pasteurii urease: an heteropolymeric enzyme with a binuclear nickel active site, Soil Biol. Biochem, 28, 819, 10.1016/0038-0717(96)00017-X Benini, 1998, Crystallization and preliminary high resolution X-ray diffraction analysis of native and β-mercaptoethanol-inhibited urease from Bacillus pasteurii, Acta Crystallogr. D, 54, 409, 10.1107/S0907444997013085 Moersdorf, 1994, EMBL Data Library, X78411, . Mulrooney, 1990, Sequence of the Klebsiella aerogenes urease genes and evidence for accessory proteins facilitating nickel incorporation, J. Bacteriol, 172, 5837, 10.1128/jb.172.10.5837-5843.1990 Benini, 1998, The complex of Bacillus pasteurii urease with β-mercaptoethanol from X-ray data at 1.65 Å resolution, J. Biol. Inorg. Chem, 3, 268, 10.1007/s007750050231 Dixon, 1975, Inhibition of jack bean urease (EC 3.5.1.5) by acetoxydroxamic acid and by phosphoramidate. An equivalent weight for urease, J. Am. Chem. Soc, 97, 4130, 10.1021/ja00847a044 Dixon, 1980, Jack bean urease (E.C. 3.5.1.5). III. The involvement of active-site nickel ion in inhibition by β-mercaptoethanol, phosphoramidate, and fluoride, Can. J. Biochem, 58, 481, 10.1139/o80-064 Todd, 1989, Competitive inhibitors of Klebsiella aerogenes urease. Mechanisms of interaction with the nickel active site, J. Biol. Chem, 264, 15835, 10.1016/S0021-9258(18)71553-6 McCarthy, 1990, Inhibition of plant and microbial ureases by phosphoramides, Plant Soil, 127, 269, 10.1007/BF00014435 Moncrief, 1995, Urease activity in the crystalline state, Protein Sci, 4, 2234, 10.1002/pro.5560041028 Allen, 1993, 3D search and research using the Cambridge Structural Database, Chemical Design Automation News, 8, 31 Basolo, 1967, Acid-Base Properties of Complex Ions Ciurli, 1996, Urease from the soil bacterium Bacillus pasteurii. 2. Immobilization on Ca-polygalacturonate, Soil Biol. & Biochem, 28, 811, 10.1016/0038-0717(96)00020-X Day, 1993, Saturation magnetization of ureases from Klebsiella aerogenes and jack bean: no evidence for exchange coupling between the two active site nickel ions in the native enzymes, Inorg. Chem, 32, 634, 10.1021/ic00057a024 Park, 1996, Characterization of the mononickel metallocenter in H134A mutant urease, J. Biol. Chem, 271, 18632, 10.1074/jbc.271.31.18632 Pearson, 1998, Chemical rescue of Klebsiella aerogenes urease variants lacking the carbamylated-lysine nickel ligand, Biochemistry, 37, 6214, 10.1021/bi980021u Jeffrey, 1991, Metrical Aspects of Three- and Four-Center Hydrogen bonds Andrews, 1986, Jack bean urease (EC 3.5.1.5). VIII. On the inhibition of urease by amides and esters of phosphoric acid, J. Am. Chem. Soc, 108, 7124, 10.1021/ja00282a059 Dixon, 1980, Jack bean urease. V. On the mechanism of action of urease on urea, formamide, acetamide, N-methylurea, and related compounds, Can. J. Biochem, 58, 1335, 10.1139/o80-181 Todd, 1987, Purification and characterization of the nickel-containing multicomponent urease from Klebsiella aerogenes, J. Biol. Chem, 262, 5963, 10.1016/S0021-9258(18)45522-6 Mobley, 1989, Microbial urease: significance, regulation and molecular characterization, Microbiol. Rev, 53, 85, 10.1128/MR.53.1.85-108.1989 Park, 1993, Site-directed mutagenesis of Klebsiella aerogenes urease: identification of hystidine residues that appear to function in nickel ligation, substrate binding, and catalysis, Protein Sci, 2, 1034, 10.1002/pro.5560020616 Park, 1993, Diethylpyrocarbonate reactivity of Klebsiella aerogenes urease: effect of pH and active site ligands on the rate of inactivation, J. Protein Chem, 12, 51, 10.1007/BF01024914 Smith, 1975, 2 Holm, 1997, An evolutionary treasure: unification of a broad set of amidohydrolases related to urease, Proteins, 28, 72, 10.1002/(SICI)1097-0134(199705)28:1<72::AID-PROT7>3.0.CO;2-L Sundell, 1994, A proposal for the catalytic mechanism in phospholipase C based on interaction energy and distance geometry calculations, Protein Eng, 7, 571, 10.1093/protein/7.4.571 Strater, 1995, Two-metal ion mechanism of bovine lens leucine aminopeptidase: active site solvent structure and binding mode of L-leucinal, a gem-diolate transition state analogue, by X-ray crystallography, Biochemistry, 34, 14792, 10.1021/bi00045a021 Kanyo, 1996, Structure of a unique binuclear manganese cluster in arginase, Nature, 283, 554, 10.1038/383554a0 Heikinheimo, 1996, A site-directed mutagenesis study of Saccharomyces cerevisiae pyrophosphatase. Functional conservation of the active site of soluble inorganic pyrophosphatases, Eur. J. Biochem, 239, 138, 10.1111/j.1432-1033.1996.0138u.x Vanhooke, 1996, Three-dimensional structure of the zinc-containing phosphotriesterase with the bound substrate analog diethyl 4-methylbenzylphosphonate, Biochemistry, 35, 6020, 10.1021/bi960325l Wilce, 1998, Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli, Proc. Natl Acad. Sci. USA, 95, 3472, 10.1073/pnas.95.7.3472 Wang, 1996, X-ray absorption spectroscopic studies of the FeZn derivative of uteroferrin, Biochemistry, 35, 13946, 10.1021/bi961436n Wilcox, 1996, Binuclear metallohydrolases, Chem. Rev, 96, 2435, 10.1021/cr950043b Dixon, 1975, Jack bean urease (EC 3.5.1.5). A metalloenzyme. A simple biological role for nickel?, J. Am. Chem. Soc, 97, 4131, 10.1021/ja00847a045 Hausinger, 1993 Andrews, 1989, Urease - A Ni(II) Metalloenzyme Mobley, 1995, Molecular biology of microbial ureases, Microbiol. Rev, 59, 451, 10.1128/MR.59.3.451-480.1995 Bremner, 1995, Recent research on problems in the use of urea as a nitrogen fertilizer, Fert. Res, 42, 321, 10.1007/BF00750524 Krogmeier, 1989, Potential phytotoxicity associated with the use of soil urease inhibitors, Proc. Natl Acad. Sci. USA, 86, 1110, 10.1073/pnas.86.4.1110 Hamilton-Miller, 1979, Rapid screening for urease inhibitors, Invest. Urol, 16, 327 Otwinowski, 1997, Processing of X-ray diffraction data collected in oscillation mode, Methods Enzymol. A, 276, 307, 10.1016/S0076-6879(97)76066-X Jones, 1991, Improved methods for building protein models in electron density maps and the location of errors in these models, Acta Cryst. A, 47, 110, 10.1107/S0108767390010224 Konnert, 1976, A restrained-parameter structure-factor least-squares refinement procedure for large asymmetric units, Acta Crystallogr. A, 32, 614, 10.1107/S0567739476001289 Konnert, 1980, A restrained-parameter thermal-factor refinement procedure, Acta Crystallogr. A, 36, 344, 10.1107/S0567739480000794 Murshudov, 1997, Refinement of macromolecular structures by the maximum-likelihood method, Acta Cryst. D, 53, 240, 10.1107/S0907444996012255 Engh, 1991, Accurate bond and angle parameters for X-ray protein structure refinement, Acta Crystallogr. A, 47, 392, 10.1107/S0108767391001071 Lamzin, 1997, Automated refinement for protein crystallography, Methods Enzymol, 277, 269, 10.1016/S0076-6879(97)77016-2 Vriend, 1990, WHATIF: a molecular modelling and drug design program, J. Molec. Graph, 8, 52, 10.1016/0263-7855(90)80070-V Laskowski, 1993, PROCHECK: a program to check the stereochemical quality of protein structures, J. Appl. Crystallogr, 26, 283, 10.1107/S0021889892009944