메뉴 건너뛰기




Volumn 47, Issue 32, 2008, Pages 8283-8291

X-ray structure of papaya chitinase reveals the substrate binding mode of glycosyl hydrolase family 19 chitinases

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CATALYSIS; COMPLEX NETWORKS; HYDROGEN BONDS; HYDROLASES; MOLECULES;

EID: 49449116267     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi800655u     Document Type: Article
Times cited : (78)

References (46)
  • 1
    • 33845250983 scopus 로고    scopus 로고
    • Pathogenesis-related proteins: Research progress in the last 15 years
    • Edreva, A. (2005) Pathogenesis-related proteins: research progress in the last 15 years. Gen. Appl. Plant Physiol. 31, 105-124.
    • (2005) Gen. Appl. Plant Physiol , vol.31 , pp. 105-124
    • Edreva, A.1
  • 2
    • 0026055308 scopus 로고
    • A classification of glycosyl hydrolase based on amino acid sequence similarities
    • Henrissat, B. (1991) A classification of glycosyl hydrolase based on amino acid sequence similarities. Biochem. J. 280, 309-316.
    • (1991) Biochem. J , vol.280 , pp. 309-316
    • Henrissat, B.1
  • 3
    • 0027225980 scopus 로고
    • New families in the classification of glycosyl hydrolases based on amino acid sequence similarities
    • Henrissat, B., and Bairoch, A. (1993) New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 293, 781-788.
    • (1993) Biochem. J , vol.293 , pp. 781-788
    • Henrissat, B.1    Bairoch, A.2
  • 4
    • 0029645404 scopus 로고
    • Structures and mechanisms of glycosyl hydrolases
    • Davies, G., and Henrissat, B. (1995) Structures and mechanisms of glycosyl hydrolases. Structure 3, 853-859.
    • (1995) Structure , vol.3 , pp. 853-859
    • Davies, G.1    Henrissat, B.2
  • 6
    • 1642521614 scopus 로고    scopus 로고
    • Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase
    • Synstad, B., Gaseidnes, S., Van Aalten, D. M. F., Vriend, G., Nielsen, J. E., and Eijsink, V. G. H. (2004) Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase. Eur. J. Biochem. 271, 253-262.
    • (2004) Eur. J. Biochem , vol.271 , pp. 253-262
    • Synstad, B.1    Gaseidnes, S.2    Van Aalten, D.M.F.3    Vriend, G.4    Nielsen, J.E.5    Eijsink, V.G.H.6
  • 7
    • 0029071185 scopus 로고
    • The refined crystal structure of an endochitinase from Hordeum vulgare L. seeds at 1.8 Å resolution
    • Hart, P. J., Pfluger, H. D., Monzingo, A. F., Hollis, T., and Robertus, J. D. (1995) The refined crystal structure of an endochitinase from Hordeum vulgare L. seeds at 1.8 Å resolution. J. Mol. Biol. 248, 402-413.
    • (1995) J. Mol. Biol , vol.248 , pp. 402-413
    • Hart, P.J.1    Pfluger, H.D.2    Monzingo, A.F.3    Hollis, T.4    Robertus, J.D.5
  • 8
    • 0028268204 scopus 로고
    • Structural similarity of plant chitinase and lysozymes from animals and phage
    • Holm, L., and Sander, C. (1994) Structural similarity of plant chitinase and lysozymes from animals and phage. FEBS Lett. 340, 129-132.
    • (1994) FEBS Lett , vol.340 , pp. 129-132
    • Holm, L.1    Sander, C.2
  • 9
    • 0030032332 scopus 로고    scopus 로고
    • Chitinases, chitosanases, and lysozymes can be divided into prokaryotic and eukaryotic families sharing a conserved core
    • Monzingo, A. F., Marcotte, E. M., Hart, P. J., and Robertus, J. D. (1996) Chitinases, chitosanases, and lysozymes can be divided into prokaryotic and eukaryotic families sharing a conserved core. Nat. Struct. Biol. 3, 133-140.
    • (1996) Nat. Struct. Biol , vol.3 , pp. 133-140
    • Monzingo, A.F.1    Marcotte, E.M.2    Hart, P.J.3    Robertus, J.D.4
  • 10
    • 0029876802 scopus 로고    scopus 로고
    • Plant chitinases use two different hydrolytic mechanisms
    • Iseli, B., Armand, S., Boller, T., Neuhaus, J.-M., and Henrissat, B. (1996) Plant chitinases use two different hydrolytic mechanisms. FEBS Lett. 382, 186-188.
    • (1996) FEBS Lett , vol.382 , pp. 186-188
    • Iseli, B.1    Armand, S.2    Boller, T.3    Neuhaus, J.-M.4    Henrissat, B.5
  • 11
    • 0034236249 scopus 로고    scopus 로고
    • Chitinolytic enzymes: Catalysis, substrate binding, and their application
    • Fukamizo, T. (2000) Chitinolytic enzymes: catalysis, substrate binding, and their application. Curr. Protein Pept. Sci. 1, 105-124.
    • (2000) Curr. Protein Pept. Sci , vol.1 , pp. 105-124
    • Fukamizo, T.1
  • 12
    • 0032516076 scopus 로고    scopus 로고
    • The role of enzyme distorsion in the single displacement mechanism of family 19 chitinases
    • Brameld, K. A., and Goddard, W. A., III (1998) The role of enzyme distorsion in the single displacement mechanism of family 19 chitinases. Proc. Natl. Acad. Sci. U.S.A. 95, 4276-4281.
    • (1998) Proc. Natl. Acad. Sci. U.S.A , vol.95 , pp. 4276-4281
    • Brameld, K.A.1    Goddard III, W.A.2
  • 13
    • 0037938666 scopus 로고    scopus 로고
    • Family 19 chitinase from rice (Oryza sativa L.): Substrate-binding subsites demonstrated by kinetic and molecular modelling studies
    • Sasaki, C., Itoh, Y., Takehara, H., Kuhara, S., and Fukamizo, T. (2003) Family 19 chitinase from rice (Oryza sativa L.): substrate-binding subsites demonstrated by kinetic and molecular modelling studies. Plant Mol. Biol. 52, 43-52.
    • (2003) Plant Mol. Biol , vol.52 , pp. 43-52
    • Sasaki, C.1    Itoh, Y.2    Takehara, H.3    Kuhara, S.4    Fukamizo, T.5
  • 16
    • 0032517353 scopus 로고    scopus 로고
    • Substrates binding sites of chitinase from barley seeds and lysozyme from goose egg white
    • Honda, Y., and Fukamizo, T. (1998) Substrates binding sites of chitinase from barley seeds and lysozyme from goose egg white. Biochem. Biophys. Acta 1388, 53-65.
    • (1998) Biochem. Biophys. Acta , vol.1388 , pp. 53-65
    • Honda, Y.1    Fukamizo, T.2
  • 18
    • 43049144994 scopus 로고    scopus 로고
    • Crystallization and X-ray analysis of a family 19 glycosyl hydrolase from Carica papaya latex
    • Huet, J., Azarkan, M., Looze, Y., Villeret, V., and Wintjens, R. (2008) Crystallization and X-ray analysis of a family 19 glycosyl hydrolase from Carica papaya latex, Acta Crystallogr. F64, 371-374.
    • (2008) Acta Crystallogr , vol.F64 , pp. 371-374
    • Huet, J.1    Azarkan, M.2    Looze, Y.3    Villeret, V.4    Wintjens, R.5
  • 19
    • 0027879008 scopus 로고
    • Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants
    • Kabsch, W. (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26, 795-800.
    • (1993) J. Appl. Crystallogr , vol.26 , pp. 795-800
    • Kabsch, W.1
  • 20
    • 0014432781 scopus 로고
    • Solvent content of protein crystals
    • Matthews, B. W. (1968) Solvent content of protein crystals. J. Mol. Biol. 33, 491-497.
    • (1968) J. Mol. Biol , vol.33 , pp. 491-497
    • Matthews, B.W.1
  • 21
    • 0028103275 scopus 로고    scopus 로고
    • The, C. C. P. 4. (1994) CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760-763.
    • The, C. C. P. 4. (1994) CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760-763.
  • 22
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Šali, A., and Blundell, T. L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815.
    • (1993) J. Mol. Biol , vol.234 , pp. 779-815
    • Šali, A.1    Blundell, T.L.2
  • 23
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: An automated program for molecular replacement
    • Vagin, A., and Teplyakov, A. (1997) MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30, 1022-1025.
    • (1997) J. Appl. Crystallogr , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 24
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building tools for molecular graphics
    • Emsley, P., and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr. D60, 2126-2132.
    • (2004) Acta Crystallogr , vol.D60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 25
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov, G. N., Vagin, A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53, 240-255.
    • (1997) Acta Crystallogr , vol.D53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.2    Dodson, E.J.3
  • 26
    • 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
  • 27
    • 0020997912 scopus 로고
    • Dictionnary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and Sander, C. (1983) Dictionnary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 28
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate diagrams of protein-ligand interactions
    • Wallace, A. C., Laskowski, R. A., and Thornton, J. M. (1995) LIGPLOT: a program to generate diagrams of protein-ligand interactions. Protein Eng. 8, 127-134.
    • (1995) Protein Eng , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 29
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald, I. K., and Thornton, J. M. (1994) Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238, 777-793.
    • (1994) J. Mol. Biol , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 30
    • 0028789439 scopus 로고
    • Optimal protein structure alignments by multiple linkage clustering: Application to distantly related proteins
    • Boutonnet, N. S., Rooman, M. J., Ochagavia, M. E., Richelle, J., and Wodak, S. J. (1995) Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins. Protein Eng. 8, 647-662.
    • (1995) Protein Eng , vol.8 , pp. 647-662
    • Boutonnet, N.S.1    Rooman, M.J.2    Ochagavia, M.E.3    Richelle, J.4    Wodak, S.J.5
  • 33
    • 34447306024 scopus 로고    scopus 로고
    • Crystal structures of a family 19 chitinase from Brassica juncea show flexibility of binding cleft loops
    • Ubhayasekera, W., Tang, C. M., Ho, S. W. T., Berglund, G., Bergfors, T., Chye, M.-L., and Mowbray, S. L. (2007) Crystal structures of a family 19 chitinase from Brassica juncea show flexibility of binding cleft loops. FEBS J. 274, 3695-3703.
    • (2007) FEBS J , vol.274 , pp. 3695-3703
    • Ubhayasekera, W.1    Tang, C.M.2    Ho, S.W.T.3    Berglund, G.4    Bergfors, T.5    Chye, M.-L.6    Mowbray, S.L.7
  • 34
    • 33750045148 scopus 로고    scopus 로고
    • Crystal structure and enzymatic properties of a bacterial family 19 chitinase reveal differences from plant enzymes
    • Hoell, I. A., Dalhus, B., Heggset, E. B., Aspmo, S. I., and Eijsink, V. G. H. (2006) Crystal structure and enzymatic properties of a bacterial family 19 chitinase reveal differences from plant enzymes. FEBS J. 273, 4889-4900.
    • (2006) FEBS J , vol.273 , pp. 4889-4900
    • Hoell, I.A.1    Dalhus, B.2    Heggset, E.B.3    Aspmo, S.I.4    Eijsink, V.G.H.5
  • 36
    • 0031574072 scopus 로고    scopus 로고
    • The clustal_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Tompson, J. D., Gilson, T. J., Plewniak, F., Janmougin, F., and Higgins, D. G. (1997) The clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24, 4876-4882.
    • (1997) Nucleic Acids Res , vol.24 , pp. 4876-4882
    • Tompson, J.D.1    Gilson, T.J.2    Plewniak, F.3    Janmougin, F.4    Higgins, D.G.5
  • 37
    • 0036186885 scopus 로고    scopus 로고
    • Expression and characterization of active site mutants of hevamine, a chitinase from the rubber tree Hevea brasiliensis
    • Bokma, E., Rozeboom, H. J., Sibbald, M., Dijkstra, B. W., and Beintema, J. J. (2002) Expression and characterization of active site mutants of hevamine, a chitinase from the rubber tree Hevea brasiliensis. Eur. J. Biochem. 269, 893-901.
    • (2002) Eur. J. Biochem , vol.269 , pp. 893-901
    • Bokma, E.1    Rozeboom, H.J.2    Sibbald, M.3    Dijkstra, B.W.4    Beintema, J.J.5
  • 40
    • 0031015902 scopus 로고    scopus 로고
    • Nomenclature for sugar-binding subsites in glycosyl hydrolases
    • Davies, G. D., Wilson, K. S., and Henrissat, B. (1997) Nomenclature for sugar-binding subsites in glycosyl hydrolases. Biochem. J. 321, 557-559.
    • (1997) Biochem. J , vol.321 , pp. 557-559
    • Davies, G.D.1    Wilson, K.S.2    Henrissat, B.3
  • 41
    • 0014199062 scopus 로고
    • The binding of oligosaccharides containing N-acetylglucosamine and N-acetylmuramic acid to lysozyme
    • Chipman, D. M., Grisaro, V., and Sharon, N. (1967) The binding of oligosaccharides containing N-acetylglucosamine and N-acetylmuramic acid to lysozyme. J. Biol. Chem. 242, 4388-4394.
    • (1967) J. Biol. Chem , vol.242 , pp. 4388-4394
    • Chipman, D.M.1    Grisaro, V.2    Sharon, N.3
  • 42
    • 0030904072 scopus 로고    scopus 로고
    • Heterologous expression and characterization of wild-type and mutant forms of a 26 Kda endochitinase from barley (Hordeum vulgare L.)
    • Andersen, M. D., Jensen, A., Robertus, J. D., Leah, R., and Skriver, K. (1997) Heterologous expression and characterization of wild-type and mutant forms of a 26 Kda endochitinase from barley (Hordeum vulgare L.). Biochem. J. 322, 815-822.
    • (1997) Biochem. J , vol.322 , pp. 815-822
    • Andersen, M.D.1    Jensen, A.2    Robertus, J.D.3    Leah, R.4    Skriver, K.5
  • 43
    • 0027226356 scopus 로고
    • Examination of the role of tyrosine-174 in the catalytic mechanism of the Arabidopsis thaliana chitinase: Comparaison of variant chitinases generated by site-directed mutagenesis and expressed in insect cells using baculovirus vectors
    • Verburg, J. G., Rangwala, S. H., Samac, D. A., Luckow, V. A., and Huynh, Q. K. (1993) Examination of the role of tyrosine-174 in the catalytic mechanism of the Arabidopsis thaliana chitinase: comparaison of variant chitinases generated by site-directed mutagenesis and expressed in insect cells using baculovirus vectors. Arch. Biochem. Biophys. 300, 223-230.
    • (1993) Arch. Biochem. Biophys , vol.300 , pp. 223-230
    • Verburg, J.G.1    Rangwala, S.H.2    Samac, D.A.3    Luckow, V.A.4    Huynh, Q.K.5
  • 44
    • 0020546727 scopus 로고
    • Amino acid sequence restriction in relation to proteolysis
    • Jörnvall, H., and Persson, B. (1983) Amino acid sequence restriction in relation to proteolysis. Biosci. Rep. 3, 225-232.
    • (1983) Biosci. Rep , vol.3 , pp. 225-232
    • Jörnvall, H.1    Persson, B.2
  • 46
    • 1442286045 scopus 로고    scopus 로고
    • Proline versus charge concept for protein stabilization against proteolytic attack
    • Markert, Y., Köditz, J., Ulbrich-Hofmann, R., and Arnold, U. (2003) Proline versus charge concept for protein stabilization against proteolytic attack. Protein Eng. 16, 1041-1046.
    • (2003) Protein Eng , vol.16 , pp. 1041-1046
    • Markert, Y.1    Köditz, J.2    Ulbrich-Hofmann, R.3    Arnold, U.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.