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Volumn 46, Issue 3, 2007, Pages 781-791

A structural factor responsible for substrate recognition by Bacillus sp. GL1 xanthan lyase that acts specifically on pyruvated side chains of xanthan

Author keywords

[No Author keywords available]

Indexed keywords

GLUCURONIC ACID; MANNOSE; PENTASACCHARIDE; XANTHAN;

EID: 33846384739     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0619775     Document Type: Article
Times cited : (19)

References (45)
  • 1
    • 0037125998 scopus 로고    scopus 로고
    • Convergent evolution sheds light on the anti-β-elimination mechanism common to family 1 and 10 polysaccharide lyases
    • Charnock, S. J., Brown, I. E., Turkenburg, J. P., Black, G. W., and Davies, G. J. (2002) Convergent evolution sheds light on the anti-β-elimination mechanism common to family 1 and 10 polysaccharide lyases, Proc. Natl. Acad. Sci. U.S.A. 99, 12067-12072.
    • (2002) Proc. Natl. Acad. Sci. U.S.A , vol.99 , pp. 12067-12072
    • Charnock, S.J.1    Brown, I.E.2    Turkenburg, J.P.3    Black, G.W.4    Davies, G.J.5
  • 2
    • 0035896032 scopus 로고    scopus 로고
    • Crystal structure of alginate lyase A1-III complexed with a trisaccharide product at 2.0 Å resolution
    • Yoon, H.-J., Hashimoto, W., Miyake, O., Murata, K., and Mikami, B. (2001) Crystal structure of alginate lyase A1-III complexed with a trisaccharide product at 2.0 Å resolution, J. Mol. Biol. 307, 9-16.
    • (2001) J. Mol. Biol , vol.307 , pp. 9-16
    • Yoon, H.-J.1    Hashimoto, W.2    Miyake, O.3    Murata, K.4    Mikami, B.5
  • 3
    • 1442265845 scopus 로고    scopus 로고
    • X-ray structural analysis of alginate lyase A1-III mutants/substrate complexes: Activation of a catalytic tyrosine residue by a flexible lid loop
    • Mikami, B., Suzuki, S., Yoon, H.-J., Miyake, O., Hashimoto, W., and Murata, K. (2002) X-ray structural analysis of alginate lyase A1-III mutants/substrate complexes: Activation of a catalytic tyrosine residue by a flexible lid loop, Acta Crystallogr. A58, C271.
    • (2002) Acta Crystallogr , vol.A58
    • Mikami, B.1    Suzuki, S.2    Yoon, H.-J.3    Miyake, O.4    Hashimoto, W.5    Murata, K.6
  • 4
    • 1442323777 scopus 로고    scopus 로고
    • High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: An enzyme-substrate complex defines the catalytic mechanism
    • Lunin, V. V., Li, Y., Linhardt, R. J., Miyazono, H., Kyogashima, M., Kaneko, T., Bell, A. W., and Cygler, M. (2004) High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: An enzyme-substrate complex defines the catalytic mechanism, J. Mol. Biol. 337, 367-386.
    • (2004) J. Mol. Biol , vol.337 , pp. 367-386
    • Lunin, V.V.1    Li, Y.2    Linhardt, R.J.3    Miyazono, H.4    Kyogashima, M.5    Kaneko, T.6    Bell, A.W.7    Cygler, M.8
  • 5
    • 21744444127 scopus 로고    scopus 로고
    • Crystal structure of Bacillus sp. GL1 xanthan lyase complexed with a substrate: Insights into the enzyme reaction mechanism
    • Maruyama, Y., Hashimoto, W., Mikami, B., and Murata, K. (2005) Crystal structure of Bacillus sp. GL1 xanthan lyase complexed with a substrate: Insights into the enzyme reaction mechanism, J. Mol. Biol. 350, 974-986.
    • (2005) J. Mol. Biol , vol.350 , pp. 974-986
    • Maruyama, Y.1    Hashimoto, W.2    Mikami, B.3    Murata, K.4
  • 6
    • 23944435850 scopus 로고    scopus 로고
    • A structural basis for depolymerization of alginate by polysaccharide lyase family-7
    • Yamasaki, M., Ogura, K., Hashimoto, W., Mikami, B., and Murata, K. (2005) A structural basis for depolymerization of alginate by polysaccharide lyase family-7, J. Mol. Biol. 352, 11-21.
    • (2005) J. Mol. Biol , vol.352 , pp. 11-21
    • Yamasaki, M.1    Ogura, K.2    Hashimoto, W.3    Mikami, B.4    Murata, K.5
  • 7
    • 33744954960 scopus 로고    scopus 로고
    • Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product
    • Shaya, D., Tocilj, A., Li, Y., Myette, J., Vankataraman, G., Sasisekharan, R., and Cygler, M. (2006) Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product, J. Biol. Chem. 281, 15525-15535.
    • (2006) J. Biol. Chem , vol.281 , pp. 15525-15535
    • Shaya, D.1    Tocilj, A.2    Li, Y.3    Myette, J.4    Vankataraman, G.5    Sasisekharan, R.6    Cygler, M.7
  • 9
    • 0016624572 scopus 로고
    • Structure of the extracellular polysaccharide from Xanthomonas campestris
    • Jansson, P.-E., Kenne, L., and Lindberg, B. (1975) Structure of the extracellular polysaccharide from Xanthomonas campestris, Carbohydr. Res. 45, 275-282.
    • (1975) Carbohydr. Res , vol.45 , pp. 275-282
    • Jansson, P.-E.1    Kenne, L.2    Lindberg, B.3
  • 10
    • 0031005018 scopus 로고    scopus 로고
    • A novel regulatory system required for pathogenicity of Xanhomonas campestris is mediated by a small diffusible signal molecule
    • Barber, C. E., Tang, J. L., Feng, J. X., Pan, M. Q., Wilson, T. J., Slaer, H., Dow, J. M., Williams, P., and Daniels, M. J. (1997) A novel regulatory system required for pathogenicity of Xanhomonas campestris is mediated by a small diffusible signal molecule, Mol. Microbiol. 24, 555-566.
    • (1997) Mol. Microbiol , vol.24 , pp. 555-566
    • Barber, C.E.1    Tang, J.L.2    Feng, J.X.3    Pan, M.Q.4    Wilson, T.J.5    Slaer, H.6    Dow, J.M.7    Williams, P.8    Daniels, M.J.9
  • 11
    • 0031557707 scopus 로고    scopus 로고
    • The Xanthomonas campestris gumD gene required for synthesis of xanthan gum is involved in normal pigmentation and virulence in causing black rot
    • Chou, F.-I., Chou, H.-C., Lin, Y.-S., Yang, B.-Y., Lin, N.-T., Weng, S.-F., and Tseng, Y.-H. (1997) The Xanthomonas campestris gumD gene required for synthesis of xanthan gum is involved in normal pigmentation and virulence in causing black rot, Biochem. Biophys. Res. Commum. 233, 265-269.
    • (1997) Biochem. Biophys. Res. Commum , vol.233 , pp. 265-269
    • Chou, F.-I.1    Chou, H.-C.2    Lin, Y.-S.3    Yang, B.-Y.4    Lin, N.-T.5    Weng, S.-F.6    Tseng, Y.-H.7
  • 12
    • 0001983273 scopus 로고
    • Bacterial polysaccharides
    • Stephan, A. M, Ed, pp, Marcel Dekker, New York
    • Morris, V. J. (1995) Bacterial polysaccharides, in Food polysaccharides and their applications (Stephan, A. M., Ed.) pp 341-375, Marcel Dekker, New York.
    • (1995) Food polysaccharides and their applications , pp. 341-375
    • Morris, V.J.1
  • 13
    • 0031688984 scopus 로고    scopus 로고
    • Xanthan gum biosynthesis and application: A biochemical/genetic perspective
    • Becker, A., Katzen, F., Puhler, A., and Ielpi, L. (1998) Xanthan gum biosynthesis and application: A biochemical/genetic perspective, Appl. Microbiol. Biotechnol. 50, 145-152.
    • (1998) Appl. Microbiol. Biotechnol , vol.50 , pp. 145-152
    • Becker, A.1    Katzen, F.2    Puhler, A.3    Ielpi, L.4
  • 14
    • 0344845209 scopus 로고    scopus 로고
    • A new in vitro assay of cholesterol adsorption by food and microbial polysaccharides
    • Soh, H.-S., Kim, C-S., and Lee, S.-P. (2003) A new in vitro assay of cholesterol adsorption by food and microbial polysaccharides, J. Med. Food 6, 225-230.
    • (2003) J. Med. Food , vol.6 , pp. 225-230
    • Soh, H.-S.1    Kim, C.-S.2    Lee, S.-P.3
  • 15
    • 7244248442 scopus 로고    scopus 로고
    • Dietary fiber suppresses elevation of uric acid and urea nitrogen concentrate ions in serum of rats with renal dysfunction induced by dietary adenine
    • Koguchi, T., Koguchi, H., Nakajima, H., Takano, S., Yamamoto, Y., Innami, S., Maekawa, A., and Tadokoro, T. (2004) Dietary fiber suppresses elevation of uric acid and urea nitrogen concentrate ions in serum of rats with renal dysfunction induced by dietary adenine, Int. J. Vitam. Nutr. Res. 74, 253-263.
    • (2004) Int. J. Vitam. Nutr. Res , vol.74 , pp. 253-263
    • Koguchi, T.1    Koguchi, H.2    Nakajima, H.3    Takano, S.4    Yamamoto, Y.5    Innami, S.6    Maekawa, A.7    Tadokoro, T.8
  • 16
    • 33846351996 scopus 로고    scopus 로고
    • Master's Thesis. Kyoto University, Kyoto, Japan
    • Miki, H. (1999) Master's Thesis. Kyoto University, Kyoto, Japan.
    • (1999)
    • Miki, H.1
  • 17
    • 0031664395 scopus 로고    scopus 로고
    • Xanthan lyase of Bacillus sp. strain GL1 liberates pyruvated mannose from xanthan side chains
    • Hashimoto, W., Miki, H., Tsuchiya, N., Nankai, H., and Murata, K. (1998) Xanthan lyase of Bacillus sp. strain GL1 liberates pyruvated mannose from xanthan side chains, Appl. Environ. Microbiol. 64, 3765-3768.
    • (1998) Appl. Environ. Microbiol , vol.64 , pp. 3765-3768
    • Hashimoto, W.1    Miki, H.2    Tsuchiya, N.3    Nankai, H.4    Murata, K.5
  • 18
    • 33646111923 scopus 로고    scopus 로고
    • Alternate structural conformations of Streptococcus pneumoniae hyaluronan lyase: Insights into enzyme flexibility and underlying molecular mechanism of action
    • Rigden, D. J., Littlejohn, J. E., Joshi, H. V., de Groot, B. L., and Jedrzejas, M. J. (2006) Alternate structural conformations of Streptococcus pneumoniae hyaluronan lyase: Insights into enzyme flexibility and underlying molecular mechanism of action, J. Mol. Biol. 358, 1165-1178.
    • (2006) J. Mol. Biol , vol.358 , pp. 1165-1178
    • Rigden, D.J.1    Littlejohn, J.E.2    Joshi, H.V.3    de Groot, B.L.4    Jedrzejas, M.J.5
  • 19
    • 0037470219 scopus 로고    scopus 로고
    • Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan
    • Hashimoto, W., Nankai, H., Mikami, B., and Murata, K. (2003) Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan, J. Biol. Chem. 278, 7663-7673.
    • (2003) J. Biol. Chem , vol.278 , pp. 7663-7673
    • Hashimoto, W.1    Nankai, H.2    Mikami, B.3    Murata, K.4
  • 20
    • 0035143725 scopus 로고    scopus 로고
    • Polysaccharide lyase: Molecular cloning, sequencing, and overexpression of the xanthan lyase gene of Bacillus sp. strain GL1
    • Hashimoto, W., Miki, H., Tsuchiya, N., Nankai, H., and Murata, K. (2001) Polysaccharide lyase: Molecular cloning, sequencing, and overexpression of the xanthan lyase gene of Bacillus sp. strain GL1, Appl. Environ. Microbiol. 67, 713-720.
    • (2001) Appl. Environ. Microbiol , vol.67 , pp. 713-720
    • Hashimoto, W.1    Miki, H.2    Tsuchiya, N.3    Nankai, H.4    Murata, K.5
  • 21
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinoski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode, Methods Enzymol. 276, 307-326.
    • (1997) Methods Enzymol , vol.276 , pp. 307-326
    • Otwinoski, Z.1    Minor, W.2
  • 23
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures, J. Appl. Crystallogr. 26, 283-291.
    • (1993) J. Appl. Crystallogr , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 24
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch, W. (1976) A solution for the best rotation to relate two sets of vectors, Acta Crystallogr. A32, 922-923.
    • (1976) Acta Crystallogr , vol.A32 , pp. 922-923
    • Kabsch, W.1
  • 25
    • 0028103275 scopus 로고    scopus 로고
    • Collaborative Computational Project, Number 4 (1994) The CCP4 suite: Programs for protein crystallography, Acta Crystallogr. D50, 760-763.
    • Collaborative Computational Project, Number 4 (1994) The CCP4 suite: Programs for protein crystallography, Acta Crystallogr. D50, 760-763.
  • 26
  • 27
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structure
    • Kraulis, P. J. (1991) MOLSCRIPT: A program to produce both detailed and schematic plots of protein structure, J. Appl. Crystallogr. 24, 946-950.
    • (1991) J. Appl. Crystallogr , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 28
    • 0028057108 scopus 로고    scopus 로고
    • Merrit, E. A, and Murphy, M. E. P, 1994 RASTER3D Version 2.0. A program for photorealistic molecular graphics, Acta Crystallogr. D50, 869-873
    • Merrit, E. A., and Murphy, M. E. P. (1994) RASTER3D Version 2.0. A program for photorealistic molecular graphics, Acta Crystallogr. D50, 869-873.
  • 29
    • 0030729838 scopus 로고    scopus 로고
    • An extensively modified version of MolScript that includes greatly enhanced coloring capabilities
    • Esnouf, R. M. (1997) An extensively modified version of MolScript that includes greatly enhanced coloring capabilities, J. Mol. Graphics Modell. 15, 132-134.
    • (1997) J. Mol. Graphics Modell , vol.15 , pp. 132-134
    • Esnouf, R.M.1
  • 32
    • 0034653873 scopus 로고    scopus 로고
    • Structural basis of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase
    • Li, S., Kelly, S. J., Lamani, E., Ferraroni, M., and Jedrzejas, M. J. (2000) Structural basis of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase, EMBO J. 15, 1228-1240.
    • (2000) EMBO J , vol.15 , pp. 1228-1240
    • Li, S.1    Kelly, S.J.2    Lamani, E.3    Ferraroni, M.4    Jedrzejas, M.J.5
  • 33
    • 0035798695 scopus 로고    scopus 로고
    • Hyaluronan binding and degradation by Streptococcus agalactiae hyaluronate lyase
    • Li, S., and Jedrzejas, M. J. (2001) Hyaluronan binding and degradation by Streptococcus agalactiae hyaluronate lyase, J. Biol. Chem. 276, 41407-41416.
    • (2001) J. Biol. Chem , vol.276 , pp. 41407-41416
    • Li, S.1    Jedrzejas, M.J.2
  • 34
    • 0037734681 scopus 로고    scopus 로고
    • Crystal structure of chondroitin AC lyase, a representative of a family of glycosaminoglycan degrading enzymes
    • Fethiere, J., Eggimann, B., and Cygler, M. (1999) Crystal structure of chondroitin AC lyase, a representative of a family of glycosaminoglycan degrading enzymes, J. Mol. Biol. 288, 635-647.
    • (1999) J. Mol. Biol , vol.288 , pp. 635-647
    • Fethiere, J.1    Eggimann, B.2    Cygler, M.3
  • 35
    • 0037414435 scopus 로고    scopus 로고
    • Crystal structure of Proteus vulgaris chondroitin sulfate ABC lyase I at 1.9 Å resolution
    • Huang, W., Lunin, V. V., Li, Y., Suzuki, S., Sugiura, N., Miyazono, H., and Cygler, M. (2003) Crystal structure of Proteus vulgaris chondroitin sulfate ABC lyase I at 1.9 Å resolution, J. Mol. Biol. 328, 623-634.
    • (2003) J. Mol. Biol , vol.328 , pp. 623-634
    • Huang, W.1    Lunin, V.V.2    Li, Y.3    Suzuki, S.4    Sugiura, N.5    Miyazono, H.6    Cygler, M.7
  • 36
    • 0037815288 scopus 로고    scopus 로고
    • Streptococcus pnermoniae hyaluronate lyase contains two non-cooperative independent folding/unfolding structural domains: Characterization of functional domain and inhibitors of enzyme
    • Akhtar, M. S., and Bhakuni, V. (2003) Streptococcus pnermoniae hyaluronate lyase contains two non-cooperative independent folding/unfolding structural domains: Characterization of functional domain and inhibitors of enzyme, J. Biol. Chem. 278, 25509-25516.
    • (2003) J. Biol. Chem , vol.278 , pp. 25509-25516
    • Akhtar, M.S.1    Bhakuni, V.2
  • 37
    • 0034953141 scopus 로고    scopus 로고
    • Kinetic properties of Streptococcus pneumoniae hyaluronate lyase
    • Kelly, S. J., Taylor, K. B., Li, S., and Jedrzejas, M. J. (2001) Kinetic properties of Streptococcus pneumoniae hyaluronate lyase, Glycobiology 11, 297-304.
    • (2001) Glycobiology , vol.11 , pp. 297-304
    • Kelly, S.J.1    Taylor, K.B.2    Li, S.3    Jedrzejas, M.J.4
  • 38
    • 0033538420 scopus 로고    scopus 로고
    • Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 Å resolution
    • Yoon, H.-J., Mikami, B., Hashimoto, W., and Murata, K. (1999) Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 Å resolution, J. Mol. Biol. 290, 505-514.
    • (1999) J. Mol. Biol , vol.290 , pp. 505-514
    • Yoon, H.-J.1    Mikami, B.2    Hashimoto, W.3    Murata, K.4
  • 39
    • 0037436378 scopus 로고    scopus 로고
    • Crystal structure and evolution of a prokaryotic glucoamylase
    • Aleshin, A. E., Feng, P.-H., Honzatko, R. B., and Reilly, P. J. (2003) Crystal structure and evolution of a prokaryotic glucoamylase, J. Mol. Biol. 327, 61-73.
    • (2003) J. Mol. Biol , vol.327 , pp. 61-73
    • Aleshin, A.E.1    Feng, P.-H.2    Honzatko, R.B.3    Reilly, P.J.4
  • 40
    • 0023910932 scopus 로고
    • Role of arginine-292 in the substrate specificity of aspartate aminotransferase as examined by site-directed mutagenesis
    • Cronin, C. N., and Kirsch, J. F. (1988) Role of arginine-292 in the substrate specificity of aspartate aminotransferase as examined by site-directed mutagenesis, Biochemistry 27, 4572-4579.
    • (1988) Biochemistry , vol.27 , pp. 4572-4579
    • Cronin, C.N.1    Kirsch, J.F.2
  • 41
    • 0028069453 scopus 로고
    • The structural basis for the altered substrate specificity of the R292D active site mutant of aspartate aminotransferase from E. coli
    • Almo, S. C., Smith, D. L., Danishefsky, A. T., and Ringe, D. (1994) The structural basis for the altered substrate specificity of the R292D active site mutant of aspartate aminotransferase from E. coli, Protein Eng. 7, 405-412.
    • (1994) Protein Eng , vol.7 , pp. 405-412
    • Almo, S.C.1    Smith, D.L.2    Danishefsky, A.T.3    Ringe, D.4
  • 42
    • 0028167665 scopus 로고
    • X-ray crystallographic study of pyridoxal 5′-phosphate-type aspartate aminotransferases from Escherichia coli in open and closed form
    • Okamoto, A., Higuchi, T., Hirotsu, K., Kuramitsu, S., and Kagamiyama. H. (1994) X-ray crystallographic study of pyridoxal 5′-phosphate-type aspartate aminotransferases from Escherichia coli in open and closed form, J. Biochem. 116, 95-101.
    • (1994) J. Biochem , vol.116 , pp. 95-101
    • Okamoto, A.1    Higuchi, T.2    Hirotsu, K.3    Kuramitsu, S.4    Kagamiyama, H.5
  • 43
    • 0030088119 scopus 로고    scopus 로고
    • Dynamic simulations of the molecular conformations of wild type and mutant xanthan polymers suggest that conformational differences may contribute to observed differences in viscosity
    • Levy, S., Schuyler, S. C., Maglothin, R. K., and Staehelin, L. A. (1996) Dynamic simulations of the molecular conformations of wild type and mutant xanthan polymers suggest that conformational differences may contribute to observed differences in viscosity, Biopolymers 38, 251-272.
    • (1996) Biopolymers , vol.38 , pp. 251-272
    • Levy, S.1    Schuyler, S.C.2    Maglothin, R.K.3    Staehelin, L.A.4
  • 44
    • 0033014632 scopus 로고    scopus 로고
    • A pyruvated mannose-specific xanthan degradation by Paenibacillus alginolyticus XL-1
    • Ruijssenaars, H. J., de Bont, J. A. M., and Hartmans, S. (1999) A pyruvated mannose-specific xanthan degradation by Paenibacillus alginolyticus XL-1, Appl. Environ. Microbiol. 65, 2446-2452.
    • (1999) Appl. Environ. Microbiol , vol.65 , pp. 2446-2452
    • Ruijssenaars, H.J.1    de Bont, J.A.M.2    Hartmans, S.3
  • 45
    • 0025875477 scopus 로고
    • Purification and characterization of a pyruvated-mannose-specific xanthan lyase from heat-stable, salt-tolerant bacteria
    • Ahlgren, J. A. (1991) Purification and characterization of a pyruvated-mannose-specific xanthan lyase from heat-stable, salt-tolerant bacteria, Appl. Environ. Microbiol. 57, 2523-2528.
    • (1991) Appl. Environ. Microbiol , vol.57 , pp. 2523-2528
    • Ahlgren, J.A.1


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