Biochemical characterization of a novel lysine racemase from Proteus mirabilis BCRC10725

Process Biochemistry

Volumn 46, Issue 10, 2011, Pages 1914-1920

  Kuan, Yi Chia ^a   Kao, Chao Hung ^b   Chen, Chao Hsien ^c   Chen, Chang Chih ^d   Hu, Hui Yu ^b   Hsu, Wen Hwei ^a  

^a NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

^b HUNGKUANG UNIVERSITY   (Taiwan)

^c CHINA MEDICAL UNIVERSITY   (Taiwan)

^d Simpson Biotech Co Ltd   (Taiwan)

Author keywords

Arginine racemization; Lysine racemase; Lysine racemization; PLP dependent enzyme; Proteus mirabilis; Substrate specificity

Indexed keywords

LYSINE RACEMIZATION; PLP-DEPENDENT ENZYME; PROTEUS MIRABILIS; RACEMASE; SUBSTRATE SPECIFICITY;

ENZYMES; ESCHERICHIA COLI; GENES;

ARGININE;

ESCHERICHIA COLI; PROTEUS MIRABILIS;

EID: 80052692104     PISSN: 13595113     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.procbio.2011.06.019     Document Type: Article

References (47)

1. C.T. Walsh Enzymes in the d-alanine branch of bacterial cell wall peptidoglycan assembly J Biol Chem 264 1989 2393 2396 (Pubitemid 19057720)
2. T. Uo, T. Yoshimura, N. Tanaka, K. Takegawa, and N. Esaki Functional characterization of alanine racemase from Schizosaccharomyces pombe: a eukaryotic counterpart to bacterial alanine racemase J Bacteriol 183 2001 2226 2233 (Pubitemid 32240391)
3. A. Hashimoto, T. Nishikawa, T. Oka, K. Takahashi, and T. Hayashi Determination of free amino acid enantiomers in rat brain and serum by high-performance liquid chromatography after derivatization with N-tert-butyloxycarbonyl-l-cysteine and o-phthaldialdehyde J Chromatogr 582 1992 41 48
4. J.J. Corrigan d-Amino acids in animals Science 164 1969 142 149
5. T. Ogawa, M. Fukuda, and K. Sasaoka Occurrence of N-malonyl-d-alanine in pea seedlings Biochim Biophys Acta 297 1973 60 69
6. M.J. Osborn Structure and biosynthesis of the bacterial cell wall Annu Rev Biochem 38 1969 501 538
7. K.H. Schleifer, and O. Kandler Peptidoglycan types of bacterial cell walls and their taxonomic implications Bacteriol Rev 36 1972 407 477
8. H. Wolosker, S. Blackshaw, and S.H. Snyder Serine racemase: a glial enzyme synthesizing d-serine to regulate glutamate-N-methyl-d-aspartate neurotransmission Proc Natl Acad Sci USA 96 1999 13409 13414
9. Y. Nagata, H. Homma, M. Matsumoto, and K. Imai Stimulation of steroidogenic acute regulatory protein (StAR) gene expression by d-aspartate in rat Leydig cells FEBS Lett 454 1999 317 320 (Pubitemid 29304623)
10. T. Yoshimura, and N. Esak Amino acid racemases: functions and mechanisms J Biosci Bioeng 96 2003 103 109 (Pubitemid 37088516)
11. S.Y. Choi, N. Esaki, M. Ashiuchi, T. Yoshimura, and K. Soda Bacterial glutamate racemase has high sequence similarity with myoglobins and forms an equimolar inactive complex with hemin Proc Natl Acad Sci USA 91 1994 10144 10147 (Pubitemid 24311965)
12. K.A. Gallo, M.E. Tanner, and J.R. Knowles Mechanism of the reaction catalyzed by glutamate racemase Biochemistry 32 1993 3991 3997 (Pubitemid 23126989)
13. P.E. Lilley, N.P. Stamford, S.G. Vasudevan, and N.E. Dixon The 92-min region of the Escherichia coli chromosome: location and cloning of the ubiA and alr genes Gene 129 1993 9 16 (Pubitemid 23208066)
14. N. Esaki, and C.T. Walsh Biosynthetic alanine racemase of Salmonella typhimurium: purification and characterization of the enzyme encoded by the alr gene Biochemistry 25 1986 3261 3267 (Pubitemid 16056968)
15. T. Oikawa, A. Tauch, S. Schaffer, and T. Fujioka Expression of alr gene from Corynebacterium glutamicum ATCC 13032 in Escherichia coli and molecular characterization of the recombinant alanine racemase J Biotechnol 125 2006 503 512 (Pubitemid 44404113)
16. K. Ono, K. Yanagida, T. Oikawa, T. Ogawa, and K. Soda Alanine racemase of alfalfa seedlings (Medicago sativa L.): first evidence for the presence of an amino acid racemase in plants Phytochemistry 67 2006 856 860 (Pubitemid 44316793)
17. J.P. Shaw, G.A. Petsko, and D. Ringe Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9- resolution Biochemistry 36 1997 1329 1342 (Pubitemid 27074957)
18. C. Schaffer, T. Wugeditsch, H. Kahlig, A. Scheberl, S. Zayni, and P. Messner The surface layer (S-layer) glycoprotein of Geobacillus stearothermophilus NRS 2004/3a. Analysis of its glycosylation J Biol Chem 277 2002 6230 6239 (Pubitemid 34968414)
19. P. LeMagueres, H. Im, A. Dvorak, U. Strych, M. Benedik, and K.L. Krause Crystal structure at 1.45 resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms Biochemistry 42 2003 14752 14761 (Pubitemid 37553503)
20. P. LeMagueres, H. Im, J. Ebalunode, U. Strych, M.J. Benedik, and J.M. Briggs The 1.9 crystal structure of alanine racemase from Mycobacterium tuberculosis contains a conserved entryway into the active site Biochemistry 44 2005 1471 1481 (Pubitemid 40204391)
21. R.M. Counago, M. Davlieva, U. Strych, R.E. Hill, and K.L. Krause Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames) BMC Struct Biol 9 2009 53
22. M. Noda, Y. Matoba, T. Kumagai, and M. Sugiyama Structural evidence that alanine racemase from a d-cycloserine-producing microorganism exhibits resistance to its own product J Biol Chem 279 2004 46153 46161 (Pubitemid 39491610)
23. U. Strych, M. Davlieva, J.P. Longtin, E.L. Murphy, H. Im, and M.J. Benedik Purification and preliminary crystallization of alanine racemase from Streptococcus pneumoniae BMC Microbiol 7 2007 40
24. A. Priyadarshi, E.H. Lee, M.W. Sung, K.H. Nam, W.H. Lee, and E.E. Kim Structural insights into the alanine racemase from Enterococcus faecalis Biochim Biophys Acta 1794 2009 1030 1040
25. A. Boniface, C. Parquet, M. Arthur, D. Mengin-Lecreulx, and D. Blanot The elucidation of the structure of Thermotoga maritima peptidoglycan reveals two novel types of cross-link J Biol Chem 284 2009 21856 21862
26. W. Vollmer, D. Blanot, and M.A. de Pedro Peptidoglycan structure and architecture FEMS Microbiol Rev 32 2008 149 167 (Pubitemid 351257814)
27. M. Guinand, J.M. Ghuysen, K.H. Schleifer, and O. Kandler The peptidoglycan in walls of Butyribacterium rettgeri Biochemistry 8 1969 200 207
28. W.E.C. Moore, and E.P. Cato Synonymy of Eubacterium limosum and Butyribacterium rettgeri: Butyribacterium limosum comb. nov Int Bull Bacteriol Nomencl Taxon 15 1965 69 80
29. H.T. Huang, D.A. Kita, and J.W. Davisson Racemization of lysine by Proteus vulgaris J Am Chem Soc 80 1958 1006 1007
30. Y.F. Chang, and E. Adams d-Lysine catabolic pathway in Pseudomonas putida: interrelations with l-lysine catabolism J Bacteriol 117 1974 753 764
31. A. Ichihara, and E.A. Ichihara Metabolism of l-lysine by bacterial enzymes J Biochem 49 1961 154 157
32. H.T. Huang, and J.W. Davisson Distribution of lysine racemase in bacteria J Bacteriol 76 1958 495 498
33. I.C. Chen, W.D. Lin, S.K. Hsu, V. Thiruvengadam, and W.H. Hsu Isolation and characterization of a novel lysine racemase from a soil metagenomic library Appl Environ Microbiol 75 2009 5161 5166
34. I.C. Chen, V. Thiruvengadam, W.D. Lin, H.H. Chang, and W.H. Hsu Lysine racemase: a novel non-antibiotic selectable marker for plant transformation Plant Mol Biol 72 2010 153 169
35. T.C. Wang, and M. Chao RNA recombination of hepatitis delta virus in natural mixed-genotype infection and transfected cultured cells J Virol 79 2005 2221 2229 (Pubitemid 40204579)
36. J. Sambrook, and D.W. Russell Molecular cloning. A laboratory manual 3rd ed. 2001 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
37. Y. Kawata, S. Yano, and H. Kojima News & notes. Efficient library construction with a TA vector and its application to cloning of the phytoene synthase gene from the cyanobacterium Spirulina platensis Curr Microbiol 37 1998 289 291 (Pubitemid 28433832)
38. A. Watanabe, Y. Kurokawa, T. Yoshimura, T. Kurihara, K. Soda, and N. Esaki Role of lysine 39 of alanine racemase from Bacillus stearothermophilus that binds pyridoxal 5′-phosphate. Chemical rescue studies of Lys39 → Ala mutant J Biol Chem 274 1999 4189 4194
39. K. Kino, M. Sato, M. Yoneyama, and K. Kirimura Synthesis of dl-tryptophan by modified broad specificity amino acid racemase from Pseudomonas putida IFO 12996 Appl Microbiol Biotechnol 73 2007 1299 1305 (Pubitemid 46089502)
40. D. Matsui, T. Oikawa, N. Arakawa, S. Osumi, F. Lausberg, and N. Stabler A periplasmic, pyridoxal-5′-phosphate-dependent amino acid racemase in Pseudomonas taetrolens Appl Microbiol Biotechnol 83 2009 1045 1054
41. S.M. Callister, and W.A. Agger Enumeration and characterization of Aeromonas hydrophila and Aeromonas caviae isolated from grocery store produce Appl Environ Microbiol 53 1987 249 253 (Pubitemid 17004602)
42. G.E. Briggs, and J.B. Haldane A note on the kinetics of enzyme action Biochem J 19 1925 338 339
43. L. Liu, K. Iwata, M. Yohda, and K. Miki Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases FEBS Lett 528 2002 114 118 (Pubitemid 35258009)
44. A. Buschiazzo, M. Goytia, F. Schaeffer, W. Degrave, W. Shepard, and C. Gregoire Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase Proc Natl Acad Sci USA 103 2006 1705 1710 (Pubitemid 43228757)
45. W.M. Patrick, J. Weisner, and J.M. Blackburn Site-directed mutagenesis of Tyr354 in Geobacillus stearothermophilus alanine racemase identifies a role in controlling substrate specificity and a possible role in the evolution of antibiotic resistance Chembiochem 3 2002 789 792 (Pubitemid 36004521)
46. S. Kanodia, S. Agarwal, P. Singh, and R. Bhatnagar Biochemical characterization of alanine racemase - a spore protein produced by Bacillus anthracis BMB Rep 42 2009 47 52
47. J. Wild, J. Hennig, M. Lobocka, W. Walczak, and T. Klopotowski Identification of the dadX gene coding for the predominant isozyme of alanine racemase in Escherichia coli K12 Mol Gen Genet 198 1985 315 322 (Pubitemid 15141833)