Isolation and molecular characterization of a novel d-hydantoinase from Jannaschia sp. CCS1

FEBS Journal

Volumn 276, Issue 13, 2009, Pages 3575-3588

  Cai, Yuanheng ^a   Trodler, Peter ^b   Jiang, Shimin ^a   Zhang, Weiwen ^c   Wu, Yan ^a   Lu, Yinhua ^a   Yang, Sheng ^a   Jiang, Weihong ^a,d  

^a Chinese Academy of Sciences   (China)

^b UNIVERSITY OF STUTTGART   (Germany)

^c ARIZONA STATE UNIVERSITY   (United States)

^d INSTITUTE PASTEUR OF SHANGHAI   (China)

Author keywords

Hydantoinase; Jannaschia sp. CCS1; Saturated mutagenesis; Structural analysis; Substrate binding pocket

Indexed keywords

AMINO ACID; DIHYDROPYRIMIDINASE;

ARTICLE; CATALYSIS; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME KINETICS; ENZYME STRUCTURE; ESCHERICHIA COLI; GENE IDENTIFICATION; JANNASCHIA; MOLECULAR DOCKING; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; PRIORITY JOURNAL; PROTEIN EXPRESSION; RHODOBACTERACEAE; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS;

AMIDOHYDROLASES; AMINO ACID SEQUENCE; ANIMALS; BACTERIAL PROTEINS; CATALYTIC DOMAIN; COMPUTER SIMULATION; GROEL PROTEIN; GROES PROTEIN; HYDROGEN-ION CONCENTRATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN STRUCTURE, TERTIARY; RHODOBACTERACEAE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY; TEMPERATURE;

ESCHERICHIA COLI; JANNASCHIA; RALSTONIA PICKETTII;

EID: 67650474097     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2009.07077.x     Document Type: Article

References (49)

1. Altenbuchner J, Siemann-Herzberg M Syldatk C (2001) Hydantoinases and related enzymes as biocatalysts for the synthesis of unnatural chiral amino acids. Curr Opin Biotechnol 12, 559 563. (Pubitemid 34146506)
2. Ogawa J Shimizu S (2002) Industrial microbial enzymes: their discovery by screening and use in large-scale production of useful chemicals in Japan. Curr Opin Biotechnol 13, 367 375. (Pubitemid 35254096)
3. Syldatk C, Läufer A, Müller R Höke H (1990) Production of optically pure d- and l-α-amino acids by bioconversion of d,l-5-monosubstituted hydantoin derivatives. Adv Biochem Eng Biot 41, 29 75.
4. Syldatk C, May O, Altenbuchner J, Mattes R Siemann M (1999) Microbial hydantoinases - industrial enzymes from the origin of life? Appl Microbiol Biotechnol 51, 293 309. (Pubitemid 29171909)
5. Park JH, Kim GJ Kim HS (2000) Production of d-amino acid using whole cells of recombinant Escherichia coli with separately and coexpressed d-hydantoinase and N-carbamoylase. Biotechnol Prog 16, 564 570.
6. Wilms B, Wiese A, Syldatk C, Mattes R Altenbuchner J (2001) Development of an Escherichia coli whole cell biocatalyst for the production of l-amino acids. J Biotechnol 86, 19 30. (Pubitemid 32167010)
7. Zrenner R, Stitt M, Sonnewald U Boldt R (2006) Pyrimidine and purine biosynthesis and degradation in plants. Annu Rev Plant Biol 57, 805 836. (Pubitemid 44061046)
8. Vogels GD Vanderdrift C (1976) Degradation of purines and pyrimidines by microorganisms. Bacteriol Rev 40, 403 468.
9. Dobritzsch D, Andersen B Piskur J (2005) Crystallization and X-ray diffraction analysis of dihydropyrimidinase from Saccharomyces kluyveri. Acta Crystallogr F Struct Biol Cryst Commun 61, 359 362. (Pubitemid 44210889)
10. Dudley KH, Butler TC Bius DL (1974) The role of dihydropyrimidinase in the metabolism of some hydantoin and succinimide drugs. Drug Metab Dispos 2, 103 112.
11. Moller A, Syldatk C, Schulze M Wagner F (1988) Stereo- and substrate-specificity of a d-hydantoinase and a d-N-carbamyl amino acid amidohydrolase of Arthrobacter crystallopoietes AM 2. Enzyme Microb Technol 10, 618 625. (Pubitemid 18246678)
12. Ogawa J Shimizu S (1997) Diversity and versatility of microbial hydantoin-transforming enzymes. J Mol Catal B Enzym 2, 163 176. (Pubitemid 127419537)
13. Bommarius AS, Schwarm M Drauz K (1998) Biocatalysis to amino acid-based chiral pharmaceuticals - examples and perspectives. J Mol Catal B-Enzym 5, 1 11. (Pubitemid 28429167)
14. Liljeblad A Kanerva LT (2006) Biocatalysis as a profound tool in the preparation of highly enantiopure beta-amino acids. Tetrahedron 62, 5831 5854. (Pubitemid 43728065)
15. Kim GJ Kim HS (1998) Identification of the structural similarity in the functionally related amidohydrolases acting on the cyclic amide ring. Biochem J 330, 295 302.
16. Lee DC, Lee SG Kim HS (1996) Production of d-p-hydroxyphenylglycine from d,l-5-(4-hydroxyphenyl)hydantoin using immobilized thermostable d-hydantoinase from Bacillus stearothermophilus SD-1. Enzyme Microb Technol 18, 35 40.
17. Hartley CJ, Kirchmann S, Burton SG Dorrington RA (1998) Production of d-amino acids from d,l-5-substituted hydantoins by an Agrobacterium tumefaciens strain and isolation of a mutant with inducer-independent expression of hydantoin-hydrolysing activity. Biotechnol Lett 20, 707 711. (Pubitemid 28389056)
18. Durr R, Vielhauer O, Burton SG, Cowan DA, Punal A, Brandao PFB, Bull AT Syldatk C (2006) Distribution of hydantoinase activity in bacterial isolates from geographically distinct environmental sources. J Mol Catal B Enzym 39, 160 165.
19. Xu Z, Liu YQ, Yang YL, Jiang WH, Arnold E Ding JP (2003) Crystal structure of d-hydantoinase from Burkholderia pickettii at a resolution of 2.7 Angstroms: insights into the molecular basis of enzyme thermostability. J Bacteriol 185, 4038 4049. (Pubitemid 36835242)
20. Nanba H, Yajima K, Takano M, Yamada Y, Ikenaka Y Takahashi S (1997) Process for producing d-N-carbamoyl-α-amino acid. European Patent Application No. EP0801131A1.
21. Abendroth J, Niefind K Schomburg D (2002) X-ray structure of a dihydropyrimidinase from Thermus sp. at 1.3 Angstrom resolution. J Mol Biol 320, 143 156. (Pubitemid 34727347)
22. Keil O, Schneider MP Rasor JP (1995) New hydantoinases from thermophilic microorganisms - synthesis of enantiomerically pure d-amino acids. Tetrahedron: Asymmetry 6, 1257 1260.
23. Lee SG, Lee DC, Sung MH Kim HS (1994) Isolation of thermostable d-hydantoinase-producing thermophilic Bacillus sp. SD-1. Biotechnol Lett 16, 461 466.
24. Kim GJ, Lee DE Kim HS (2000) Functional expression and characterization of the two cyclic amidohydrolase enzymes, allantoinase and a novel phenylhydantoinase, from Escherichia coli. J Bacteriol 182, 7021 7028. (Pubitemid 32259606)
25. Nam SH, Park HS Kim HS (2005) Evolutionary relationship and application of a superfamily of cyclic amidohydrolase enzymes. Chem Rec 5, 298 307.
26. Wiederstein M Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35, W407 W410.
27. Cheon YH, Kim HS, Han KH, Abendroth J, Niefind K, Schomburg D, Wang JM Kim Y (2002) Crystal structure of d-hydantoinase from Bacillus stearothermophilus: insight into the stereochemistry of enantioselectivity. Biochemistry 41, 9410 9417. (Pubitemid 34810015)
28. Hermann JC, Ghanem E, Li YC, Raushel FM, Irwin JJ Shoichet BK (2006) Predicting substrates by docking high-energy intermediates to enzyme structures. J Am Chem Soc 128, 15882 15891. (Pubitemid 44894131)
29. Goloubinoff P, Gatenby AA Lorimer GH (1989) GroE heat-shock proteins promote assembly of foreign prokaryotic ribulose bisphosphate carboxylase oligomers in Escherichia coli. Nature 337, 44 47. (Pubitemid 19022550)
30. Caspers P, Stieger M Burn P (1994) Overproduction of bacterial chaperones improves the solubility of recombinant protein-tyrosine kinases in Escherichia coli. Cell Mol Biol 40, 635 644.
31. Jiang SM, Li CH, Zhang WW, Cai YH, Yang YL, Yang S Jiang WH (2007) Directed evolution and structural analysis of N-carbamoyl-d-amino acid amidohydrolase provide insights into recombinant protein solubility in Escherichia coli. Biochem J 402, 429 437. (Pubitemid 46423880)
32. Syldatk C, Cotoras D, Dombach G, Gro C, Kallwa H Wagner F (1987) Substrate- and stereospecificity, induction and metallo-dependence of a microbial hydantoinase. Biotechnol Lett 9, 25 30. (Pubitemid 17000423)
33. Lohkamp B, Andersen B, Piskur J Dobritzsch D (2006) The crystal structures of dihydropyrimidinases reaffirm the close relationship between cyclic amidohydrolases and explain their substrate specificity. J Biol Chem 281, 13762 13776. (Pubitemid 43855292)
34. Abendroth J, Niefind K, May O, Siemann M, Syldatk C Schomburg D (2002) The structure of l-hydantoinase from Arthobacter aurescens leads to an understanding of dihydropyrimidinase substrate and enantio specificity. Biochemistry 41, 8589 8597. (Pubitemid 34745999)
35. Cheon YH, Park HS, Lee SC, Lee DE Kim HS (2003) Structure-based mutational analysis of the active site residues of d-hydantoinase. J Mol Catal B Enzym 26, 217 222.
36. 8-barrel protein, for modulation of the substrate specificity. Biochemistry 43, 7413 7420. (Pubitemid 38745758)
37. Chao YP, Chiang CJ, Lo TE Fu H (2000) Overproduction of d-hydantoinase and carbamoylase in a soluble form in Escherichia coli. Appl Microbiol Biotechnol 54, 348 353. (Pubitemid 30737480)
38. Wallach DP Grisolia S (1957) The purification and properties of hydropyrimidine hydrase. J Biol Chem 226, 277 288.
39. Thompson JD, Higgins DG Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673 4680. (Pubitemid 24354800)
40. Sambrook J Russell DW (2000) Molecular Cloning: A Laboratory Manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
41. Bradford MM (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.
42. Runser SM Meyer PC (1993) Purification and biochemical-characterization of the hydantoin hydrolyzing enzyme from Agrobacterium species - a hydantoinase with no 5,6-dihydropyrimidine amidohydrolase activity. Eur J Biochem 213, 1315 1324. (Pubitemid 23152243)
43. Schwede T, Kopp J, Guex N Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 31, 3381 3385. (Pubitemid 37442164)
44. Notredame C, Higgins DG Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302, 205 217. (Pubitemid 30694431)
45. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19, 1639 1662. (Pubitemid 128590223)
46. Gasteiger J, Rudolph C Sadowski J (1990) Automatic generation of 3D-atomic coordinates for organic molecules. Tetrahedron Comput Method 3, 537 547.
47. Hammarström L-G, Liljefors T Gasteiger J (1988) Electrostatic interactions in molecular mechanics (MM2) calculations via PEOE partial charges I. Haloalkanes. J Comput Chem 9, 424 440.
48. Hu X Shelver WH (2003) Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction. J Mol Graph Model 22, 115 126. (Pubitemid 36976838)
49. Lee M, Maher MJ Guss JM (2007) Structure of the T109S mutant of Escherichia coli dihydroorotase complexed with the inhibitor 5-fluoroorotate: catalytic activity is reflected by the crystal form. Acta Crystallogr F Struct Biol Cryst Commun 63, 154 161. (Pubitemid 46438674)