Seiji Negoro

Summary

Affiliation: University of Hyogo
Country: Japan

Publications

  1. ncbi request reprint X-ray crystallographic analysis of 6-aminohexanoate-dimer hydrolase: molecular basis for the birth of a nylon oligomer-degrading enzyme
    Seiji Negoro
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
    J Biol Chem 280:39644-52. 2005
  2. pmc 6-Aminohexanoate oligomer hydrolases from the alkalophilic bacteria Agromyces sp. strain KY5R and Kocuria sp. strain KY2
    Kengo Yasuhira
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2280, Japan
    Appl Environ Microbiol 73:7099-102. 2007
  3. ncbi request reprint Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase
    Seiji Negoro
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2280, Japan
    J Mol Biol 370:142-56. 2007
  4. pmc Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a beta-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase
    Taku Ohki
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Hyogo 671 2280, Japan
    Protein Sci 18:1662-73. 2009
  5. pmc X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation
    Kengo Yasuhira
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Hyogo 671 2201, Japan
    J Biol Chem 285:1239-48. 2010
  6. doi request reprint Molecular design of a nylon-6 byproduct-degrading enzyme from a carboxylesterase with a beta-lactamase fold
    Yasuyuki Kawashima
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Japan
    FEBS J 276:2547-56. 2009
  7. ncbi request reprint Mutational analysis of 6-aminohexanoate-dimer hydrolase: relationship between nylon oligomer hydrolytic and esterolytic activities
    Taku Ohki
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2280, Japan
    FEBS Lett 580:5054-8. 2006
  8. pmc Three-dimensional structure of nylon hydrolase and mechanism of nylon-6 hydrolysis
    Seiji Negoro
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Hyogo 671 2280
    J Biol Chem 287:5079-90. 2012
  9. ncbi request reprint Comparison of acyl-CoA synthetic activities and enantioselectivity toward 2-arylpropanoic acids in firefly luciferases
    Dai ichiro Kato
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo
    Biosci Biotechnol Biochem 75:1758-62. 2011
  10. pmc Crystallization and X-ray diffraction analysis of nylon-oligomer hydrolase (NylC) from Agromyces sp. KY5R
    Kengo Yasuhira
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 67:892-5. 2011

Collaborators

Detail Information

Publications24

  1. ncbi request reprint X-ray crystallographic analysis of 6-aminohexanoate-dimer hydrolase: molecular basis for the birth of a nylon oligomer-degrading enzyme
    Seiji Negoro
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
    J Biol Chem 280:39644-52. 2005
    ..Here, we propose that amino acid replacements in the catalytic cleft of a preexisting esterase with the beta-lactamase fold resulted in the evolution of the nylon oligomer hydrolase...
  2. pmc 6-Aminohexanoate oligomer hydrolases from the alkalophilic bacteria Agromyces sp. strain KY5R and Kocuria sp. strain KY2
    Kengo Yasuhira
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2280, Japan
    Appl Environ Microbiol 73:7099-102. 2007
    ..6% similarity to the enzyme in neutrophilic Arthrobacter sp. but had superior thermostability, activity under alkaline conditions, and affinity for nylon-related substrates, which would be advantageous for biotechnological applications...
  3. ncbi request reprint Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase
    Seiji Negoro
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2280, Japan
    J Mol Biol 370:142-56. 2007
    ..Present models illustrate why new activity against the nylon oligomer has evolved in an esterase with beta-lactamase folds, while retaining the original esterolytic functions...
  4. pmc Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a beta-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase
    Taku Ohki
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Hyogo 671 2280, Japan
    Protein Sci 18:1662-73. 2009
    ..FEBS J 2009; 276:2547-2556). We propose here that there exist at least two alternative modes for optimizing the Ald-hydrolytic activity of a carboxylesterase with a beta-lactamase fold...
  5. pmc X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation
    Kengo Yasuhira
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Hyogo 671 2201, Japan
    J Biol Chem 285:1239-48. 2010
    ..On the basis of the structure and functional analysis, we discussed the catalytic mechanisms and evolution of NylA in comparison with other Ser-reactive hydrolases...
  6. doi request reprint Molecular design of a nylon-6 byproduct-degrading enzyme from a carboxylesterase with a beta-lactamase fold
    Yasuyuki Kawashima
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Japan
    FEBS J 276:2547-56. 2009
    ....
  7. ncbi request reprint Mutational analysis of 6-aminohexanoate-dimer hydrolase: relationship between nylon oligomer hydrolytic and esterolytic activities
    Taku Ohki
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2280, Japan
    FEBS Lett 580:5054-8. 2006
    ..D370Y increased esterolytic activity for glycerylbutyrate ca. 30-50-fold, whereas G181D decreased the activity to 30% of the parental enzyme...
  8. pmc Three-dimensional structure of nylon hydrolase and mechanism of nylon-6 hydrolysis
    Seiji Negoro
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Hyogo 671 2280
    J Biol Chem 287:5079-90. 2012
    ..Based on these data, we propose that NylC should be designated as nylon hydrolase (or nylonase). Three potential uses of NylC for industrial and environmental applications are also discussed...
  9. ncbi request reprint Comparison of acyl-CoA synthetic activities and enantioselectivity toward 2-arylpropanoic acids in firefly luciferases
    Dai ichiro Kato
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo
    Biosci Biotechnol Biochem 75:1758-62. 2011
    ..In addition, by determining the kinetic parameters at various pH values, we verified that the k(cat) parameter contributed to the preferential enantioselectivity of this enzyme...
  10. pmc Crystallization and X-ray diffraction analysis of nylon-oligomer hydrolase (NylC) from Agromyces sp. KY5R
    Kengo Yasuhira
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 67:892-5. 2011
    ..86, b = 214.45, c = 478.80 Å. The anomalous difference Patterson map of the K(2)PtCl(4)-derivative crystal suggested that the space group was I222 rather than I2(1)2(1)2(1)...
  11. doi request reprint Identification and characterization of another 4-nitrophenol degradation gene cluster, nps, in Rhodococcus sp. strain PN1
    Kenta Yamamoto
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2280, Japan
    J Biosci Bioeng 111:687-94. 2011
    ..These results indicate that this nps gene cluster, in addition to the nph gene cluster, is also involved in 4-NP degradation in strain PN1...
  12. pmc Crystallization and X-ray diffraction analysis of 6-aminohexanoate-dimer hydrolase from Arthrobacter sp. KI72
    Taku Ohki
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2201, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:928-30. 2005
    ..37, c = 113.09 A. Diffraction data were collected from native and methylmercuric chloride derivative crystals to resolutions of 1.75 and 1.80 A, respectively...
  13. pmc Crystallization and X-ray diffraction analysis of 6-aminohexanoate-cyclic-dimer hydrolase from Arthrobacter sp. KI72
    Kengo Yasuhira
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2280, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:1209-11. 2006
    ..0. The crystal is hexagonal, with unit-cell parameters a = b = 130.75, c = 58.23 A. Diffraction data were collected from native and mercury(II) dichloride-derivative crystals to resolutions of 1.90 and 2.06 A, respectively...
  14. ncbi request reprint Immunoassay using microfluid filters constructed by deep X-ray lithography
    Katsuhiro Matsui
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
    Biosci Biotechnol Biochem 71:3098-101. 2007
    ....
  15. ncbi request reprint Purification and characterization of alkylcatechol 2,3-dioxygenase from butylphenol degradation pathway of Pseudomonas putida MT4
    Masahiro Takeo
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2201, Japan
    J Biosci Bioeng 104:309-14. 2007
    ..4, 8.4, and 6.5 microM and 25.8, 76.9, and 18.0 U mg(-1), respectively. These results suggest that BupB has broad substrate specificity for 4-n-alkylcatechols...
  16. pmc Mechanism of 4-nitrophenol oxidation in Rhodococcus sp. Strain PN1: characterization of the two-component 4-nitrophenol hydroxylase and regulation of its expression
    Masahiro Takeo
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2201, Japan
    J Bacteriol 190:7367-74. 2008
    ..The 4-NP hydroxylase showed comparable oxidation activities for phenol and 4-chlorophenol to that for 4-NP and weaker activities for 3-NP and 4-NC...
  17. ncbi request reprint Purification and gene cloning of an enantioselective thioesterification enzyme from Brevibacterium ketoglutamicum KU1073, a deracemization bacterium of 2-(4-chlorophenoxy)propanoic acid
    Dai ichiro Kato
    Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
    Biosci Biotechnol Biochem 74:2405-12. 2010
    ..This result indicates that MCAD1 should be classified into a family of medium-chain acyl-CoA synthetase. This novel activity has never been reported for this family...
  18. ncbi request reprint New application of firefly luciferase--it can catalyze the enantioselective thioester formation of 2-arylpropanoic acid
    Dai ichiro Kato
    Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
    FEBS J 274:3877-85. 2007
    ..These results suggest that LUC-H could catalyze the kinetic resolution of 2-arylpropanoic acid efficiently and would be a new option for the preparation of optically active 2-substituted carboxylic acids...
  19. doi request reprint Two identical nonylphenol monooxygenase genes linked to IS6100 and some putative insertion sequence elements in Sphingomonas sp. NP5
    Masahiro Takeo
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2280, Japan
    Microbiology 158:1796-807. 2012
    ..3-Methyl-3-octanol, probably originating from the alkyl side chain, was also detected as the metabolite. These results indicate that these two nmoA genes are involved in the NP degradation ability of strain NP5...
  20. doi request reprint Genetic organization of nylon-oligomer-degrading enzymes from alkalophilic bacterium, Agromyces sp. KY5R
    Kengo Yasuhira
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2280, Japan
    J Biosci Bioeng 104:521-4. 2007
    ..However, we found several genetic rearrangements between the two DNA regions. Here, we discuss the possible mechanisms underlying the genetic rearrangements...
  21. doi request reprint Function of a Glutamine Synthetase-Like Protein in Bacterial Aniline Oxidation via γ-Glutamylanilide
    Masahiro Takeo
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
    J Bacteriol 195:4406-14. 2013
    ....
  22. ncbi request reprint Enzyme-linked immunosorbent assay for nonylphenol using antibody-bound microfluid filters in vertical fluidic operation
    Katsuhiro Matsui
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2280, Japan
    J Biosci Bioeng 104:347-50. 2007
    ..Through the optimization of the immunoassay, nonylphenol was quantitatively detected at the range of 0.1-10 ng/ml...
  23. ncbi request reprint Characterization of alkylphenol degradation gene cluster in Pseudomonas putida MT4 and evidence of oxidation of alkylphenols and alkylcatechols with medium-length alkyl chain
    Masahiro Takeo
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671 2201, Japan
    J Biosci Bioeng 102:352-61. 2006
    ..These results suggest that MT4 is a very useful strain in the biodegradation of a wide range of APs with a medium-length alkyl chain, which known nonylphenol-degrading Sphingomonas strains have never degraded...
  24. ncbi request reprint Purification and characterization of catechol 2,3-dioxygenase from the aniline degradation pathway of Acinetobacter sp. YAA and its mutant enzyme, which resists substrate inhibition
    Masahiro Takeo
    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
    Biosci Biotechnol Biochem 71:1668-75. 2007
    ..Kinetic analysis of these enzymes revealed that the wild-type enzyme suffered from substrate inhibition at >2 microM, while the mutant enzyme loosened substrate inhibition...