메뉴 건너뛰기




Volumn 328, Issue 3, 2003, Pages 635-654

Crystal structure of thermostable aspartase from Bacillus sp. YM55-1: Structure-based exploration of functional sites in the aspartase family

Author keywords

Aspartase; Crystal structure; High activity; Local structural comparison; Thermostability

Indexed keywords

ALPHA AMINO ACID; ASPARTATE AMMONIA LYASE; BACTERIAL ENZYME; FUMARATE HYDRATASE; GLUTAMINE; GLYCINE; LYSINE;

EID: 0037414436     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00310-3     Document Type: Article
Times cited : (28)

References (57)
  • 3
    • 0015902723 scopus 로고
    • Studies on aspartase. I. Purification and molecular properties of aspartase from Escherichia coli
    • Suzuki S., Yamaguchi J., Tokushige M. Studies on aspartase. I. Purification and molecular properties of aspartase from Escherichia coli. Biochim. Biophys. Acta. 321:1973;369-381.
    • (1973) Biochim. Biophys. Acta , vol.321 , pp. 369-381
    • Suzuki, S.1    Yamaguchi, J.2    Tokushige, M.3
  • 4
    • 0025903701 scopus 로고
    • Kinetic studies of L-aspartase from Escherichia coli: PH-dependent activity changes
    • Karsten W.E., Viola R.E. Kinetic studies of L-aspartase from Escherichia coli: pH-dependent activity changes. Arch. Biochem. Biophys. 287:1991;60-67.
    • (1991) Arch. Biochem. Biophys. , vol.287 , pp. 60-67
    • Karsten, W.E.1    Viola, R.E.2
  • 5
    • 0022549346 scopus 로고
    • Kinetic studies of L-aspartase from Escherichia coli: Substrate activation
    • Karsten W.E., Gates R.B., Viola R.E. Kinetic studies of L-aspartase from Escherichia coli: substrate activation. Biochemistry. 25:1986;1299-1303.
    • (1986) Biochemistry , vol.25 , pp. 1299-1303
    • Karsten, W.E.1    Gates, R.B.2    Viola, R.E.3
  • 6
    • 0021875577 scopus 로고
    • L-Aspartate-induced activation of aspartase
    • Ida N., Tokushige M. L-Aspartate-induced activation of aspartase. J. Biochem. 98:1985;35-39.
    • (1985) J. Biochem. , vol.98 , pp. 35-39
    • Ida, N.1    Tokushige, M.2
  • 8
    • 0022474612 scopus 로고
    • Structural and functional relationships between fumarase and aspartase. Nucleotide sequences of the fumarase (fumC) and aspartase (aspA) genes of Escherichia coli K12
    • Woods S.A., Miles J.S., Roberts R.E., Guest J.R. Structural and functional relationships between fumarase and aspartase. Nucleotide sequences of the fumarase (fumC) and aspartase (aspA) genes of Escherichia coli K12. Biochem. J. 237:1986;547-557.
    • (1986) Biochem. J. , vol.237 , pp. 547-557
    • Woods, S.A.1    Miles, J.S.2    Roberts, R.E.3    Guest, J.R.4
  • 9
    • 0000127854 scopus 로고
    • Sequence homologies between argininosuccinase, aspartase and fumarase: A family of structurally-related enzymes
    • Woods S.A., Miles J.S., Guest J.R. Sequence homologies between argininosuccinase, aspartase and fumarase: a family of structurally-related enzymes. FEMS Microbiol. Letters. 51:1988;181-186.
    • (1988) FEMS Microbiol. Letters , vol.51 , pp. 181-186
    • Woods, S.A.1    Miles, J.S.2    Guest, J.R.3
  • 10
    • 0028198853 scopus 로고
    • Mutagenic investigation of conserved functional amino acids in Escherichia coli L-aspartase
    • Saribas A.S., Schindler J.F., Viola R.E. Mutagenic investigation of conserved functional amino acids in Escherichia coli L-aspartase. J. Biol. Chem. 269:1994;6313-6319.
    • (1994) J. Biol. Chem. , vol.269 , pp. 6313-6319
    • Saribas, A.S.1    Schindler, J.F.2    Viola, R.E.3
  • 11
    • 0030877622 scopus 로고    scopus 로고
    • Evaluation of functionally important amino acids in L-aspartate ammonia-lyase from Escherichia coli
    • Jayasekera M.M.K., Shi W., Farber G.K., Viola R.E. Evaluation of functionally important amino acids in L-aspartate ammonia-lyase from Escherichia coli. Biochemistry. 36:1997;9145-9150.
    • (1997) Biochemistry , vol.36 , pp. 9145-9150
    • Jayasekera, M.M.K.1    Shi, W.2    Farber, G.K.3    Viola, R.E.4
  • 12
    • 0016802754 scopus 로고
    • Studies on aspartase II. Role of sulfhydryl groups in aspartase from Escherichia coli
    • Mizuta K., Tokushige M. Studies on aspartase II. Role of sulfhydryl groups in aspartase from Escherichia coli. Biochim. Biophys. Acta. 403:1975;221-231.
    • (1975) Biochim. Biophys. Acta , vol.403 , pp. 221-231
    • Mizuta, K.1    Tokushige, M.2
  • 13
    • 0021525866 scopus 로고
    • Chemical modification of essential histidine residues in aspartase with diethylpyrocarbonate
    • Ida N., Tokushige M. Chemical modification of essential histidine residues in aspartase with diethylpyrocarbonate. J. Biochem. 96:1984;1315-1321.
    • (1984) J. Biochem. , vol.96 , pp. 1315-1321
    • Ida, N.1    Tokushige, M.2
  • 14
    • 0022413995 scopus 로고
    • Assignment of catalytically essential cysteine residues in aspartase by selective chemical modification with N-(7-dimethylamino-4-methylcoumarynyl)maleimide
    • Ida N., Tokushige M. Assignment of catalytically essential cysteine residues in aspartase by selective chemical modification with N-(7-dimethylamino-4-methylcoumarynyl)maleimide. J. Biochem. 98:1985;793-797.
    • (1985) J. Biochem. , vol.98 , pp. 793-797
    • Ida, N.1    Tokushige, M.2
  • 15
    • 0028928466 scopus 로고
    • Elimination of the sensitivity of L-aspartase to active-site-directed inactivation without alteration of catalytic activity
    • Giorgianni F., Beranová S., Wesdemiotis C., Viola R.E. Elimination of the sensitivity of L-aspartase to active-site-directed inactivation without alteration of catalytic activity. Biochemistry. 34:1995;3529-3535.
    • (1995) Biochemistry , vol.34 , pp. 3529-3535
    • Giorgianni, F.1    Beranová, S.2    Wesdemiotis, C.3    Viola, R.E.4
  • 16
    • 0031570306 scopus 로고    scopus 로고
    • Mapping the mechanism-based modification sites in L-aspartase from Escherichia coli
    • Giorgianni F., Beranová S., Wesdemiotis C., Viola R.E. Mapping the mechanism-based modification sites in L-aspartase from Escherichia coli. Arch. Biochem. Biophys. 341:1997;329-336.
    • (1997) Arch. Biochem. Biophys. , vol.341 , pp. 329-336
    • Giorgianni, F.1    Beranová, S.2    Wesdemiotis, C.3    Viola, R.E.4
  • 18
    • 0030848314 scopus 로고    scopus 로고
    • Human argininosuccinate lyase: A structural basis for intragenic complementation
    • Turner M.A., Simpson A., McInnes R.R., Howell P.L. Human argininosuccinate lyase: a structural basis for intragenic complementation. Proc. Natl Acad. Sci. USA. 94:1997;9063-9068.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 9063-9068
    • Turner, M.A.1    Simpson, A.2    McInnes, R.R.3    Howell, P.L.4
  • 19
    • 0034651835 scopus 로고    scopus 로고
    • The structure of adenylosuccinate lyase, an enzyme with dual activity in the de novo purine biosynthetic pathway
    • Toth E.A., Yeates T.O. The structure of adenylosuccinate lyase, an enzyme with dual activity in the de novo purine biosynthetic pathway. Structure. 8:2000;163-174.
    • (2000) Structure , vol.8 , pp. 163-174
    • Toth, E.A.1    Yeates, T.O.2
  • 20
    • 0028518695 scopus 로고
    • The structure of avian eye lens δ-crystallin reveals a new fold for a superfamily of oligomeric enzymes
    • Simpson A., Bateman O., Driessen H., Lindley P., Moss D., Mylvaganam S., et al. The structure of avian eye lens δ-crystallin reveals a new fold for a superfamily of oligomeric enzymes. Nature Struct. Biol. 1:1994;724-734.
    • (1994) Nature Struct. Biol. , vol.1 , pp. 724-734
    • Simpson, A.1    Bateman, O.2    Driessen, H.3    Lindley, P.4    Moss, D.5    Mylvaganam, S.6
  • 21
    • 0026794264 scopus 로고
    • 3-Carboxy-cis,cis-muconate lactonizing enzyme from Pseudomonas putida is homologous to the class II fumarase family: A new reaction in the evolution of a mechanistic motif
    • Williams S.E., Woolridge E.M., Ransom S.C., Landro J.A., Babbitt P.C., Kozarich J.W. 3-Carboxy-cis,cis-muconate lactonizing enzyme from Pseudomonas putida is homologous to the class II fumarase family: a new reaction in the evolution of a mechanistic motif. Biochemistry. 31:1992;9768-9776.
    • (1992) Biochemistry , vol.31 , pp. 9768-9776
    • Williams, S.E.1    Woolridge, E.M.2    Ransom, S.C.3    Landro, J.A.4    Babbitt, P.C.5    Kozarich, J.W.6
  • 23
    • 0019332560 scopus 로고
    • 3-Carbanionic substrate analogues bind very tightly to fumarase and aspartase
    • Porter D.J.T., Bright H.J. 3-Carbanionic substrate analogues bind very tightly to fumarase and aspartase. J. Biol. Chem. 255:1980;4772-4780.
    • (1980) J. Biol. Chem. , vol.255 , pp. 4772-4780
    • Porter, D.J.T.1    Bright, H.J.2
  • 24
    • 0021769539 scopus 로고
    • Kinetic mechanism and location of rate-determining steps for aspartase from Hafnia alvei
    • Nuiry I.I., Hermes J.D., Weiss P.M., Chen C.-Y., Cook P.F. Kinetic mechanism and location of rate-determining steps for aspartase from Hafnia alvei. Biochemistry. 23:1984;5168-5175.
    • (1984) Biochemistry , vol.23 , pp. 5168-5175
    • Nuiry, I.I.1    Hermes, J.D.2    Weiss, P.M.3    Chen, C.-Y.4    Cook, P.F.5
  • 25
    • 0033150884 scopus 로고    scopus 로고
    • Purification and characterization of thermostable aspartase from Bacillus sp YM55-1
    • Kawata Y., Tamura K., Yano S., Mizobata T., Nagai J., Esaki N., et al. Purification and characterization of thermostable aspartase from Bacillus sp YM55-1. Arch. Biochem. Biophys. 366:1999;40-46.
    • (1999) Arch. Biochem. Biophys. , vol.366 , pp. 40-46
    • Kawata, Y.1    Tamura, K.2    Yano, S.3    Mizobata, T.4    Nagai, J.5    Esaki, N.6
  • 26
    • 0034021294 scopus 로고    scopus 로고
    • Cloning and over-expression of thermostable Bacillus sp. YM55-1 aspartase and site-directed mutagenesis for probing a catalytic residue
    • Kawata Y., Tamura K., Kawamura M., Ikei K., Mizobata T., Nagai J., et al. Cloning and over-expression of thermostable Bacillus sp. YM55-1 aspartase and site-directed mutagenesis for probing a catalytic residue. Eur. J. Biochem. 267:2000;1847-1857.
    • (2000) Eur. J. Biochem. , vol.267 , pp. 1847-1857
    • Kawata, Y.1    Tamura, K.2    Kawamura, M.3    Ikei, K.4    Mizobata, T.5    Nagai, J.6
  • 27
    • 0029854921 scopus 로고    scopus 로고
    • Crystallographic studies of the catalytic and a second site in fumarase C from Escherichia coli
    • Weaver T., Banaszak L. Crystallographic studies of the catalytic and a second site in fumarase C from Escherichia coli. Biochemistry. 35:1996;13955-13965.
    • (1996) Biochemistry , vol.35 , pp. 13955-13965
    • Weaver, T.1    Banaszak, L.2
  • 28
    • 0030938063 scopus 로고    scopus 로고
    • Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid biding site
    • Weaver T., Lees M., Banaszak L. Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid biding site. Protein Sci. 6:1997;834-842.
    • (1997) Protein Sci. , vol.6 , pp. 834-842
    • Weaver, T.1    Lees, M.2    Banaszak, L.3
  • 29
    • 0032527680 scopus 로고    scopus 로고
    • Chemical mechanism of the endogenous argininosuccinate lyase activity of duck lens δ2-crystallin
    • Wu C.-Y., Lee H.-J., Wu S.-H., Chen S.-T., Chiou S.-H., Chang G.-G. Chemical mechanism of the endogenous argininosuccinate lyase activity of duck lens δ2-crystallin. Biochem. J. 333:1998;327-334.
    • (1998) Biochem. J. , vol.333 , pp. 327-334
    • Wu, C.-Y.1    Lee, H.-J.2    Wu, S.-H.3    Chen, S.-T.4    Chiou, S.-H.5    Chang, G.-G.6
  • 30
    • 0033524224 scopus 로고    scopus 로고
    • 141 are critical contributors to the intersubunit catalytic site of adenylosuccinate lyase of Bacillus subtilis
    • 141 are critical contributors to the intersubunit catalytic site of adenylosuccinate lyase of Bacillus subtilis. Biochemistry. 38:1999;22-32.
    • (1999) Biochemistry , vol.38 , pp. 22-32
    • Lee, T.T.1    Worby, C.2    Bao, Z.-Q.3    Dixon, J.E.4    Colman, R.F.5
  • 31
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski R.A. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.
    • (1993) J. Appl. Crystallog. , vol.26 , pp. 283-291
    • Laskowski, R.A.1
  • 33
    • 0033596741 scopus 로고    scopus 로고
    • Crystal structure of an inactive duck δ II crystallin mutant with bound argininosuccinate
    • Vallée F., Turner M.A., Lindley P.L., Howell P.L. Crystal structure of an inactive duck δ II crystallin mutant with bound argininosuccinate. Biochemistry. 38:1999;2425-2434.
    • (1999) Biochemistry , vol.38 , pp. 2425-2434
    • Vallée, F.1    Turner, M.A.2    Lindley, P.L.3    Howell, P.L.4
  • 34
    • 0029073551 scopus 로고
    • Exploring the role of histidines in the catalytic activity of duck δ-crystallins using site-directed mutagenesis
    • Patejunas G., Barbosa P., Lacombe M., O'Brien W.E. Exploring the role of histidines in the catalytic activity of duck δ-crystallins using site-directed mutagenesis. Expt. Eye Res. 61:1995;151-154.
    • (1995) Expt. Eye Res. , vol.61 , pp. 151-154
    • Patejunas, G.1    Barbosa, P.2    Lacombe, M.3    O'Brien, W.E.4
  • 35
    • 0019157471 scopus 로고
    • Use of isotope effects to deduce the chemical mechanism of fumarase
    • Blanchard J.S., Cleland W.W. Use of isotope effects to deduce the chemical mechanism of fumarase. Biochemistry. 19:1980;4506-4513.
    • (1980) Biochemistry , vol.19 , pp. 4506-4513
    • Blanchard, J.S.1    Cleland, W.W.2
  • 36
    • 0024298585 scopus 로고
    • L-Aspartase from Escherichia coli: Substrate specificity and role of divalent metal ions
    • Falzone C.J., Karsten W.E., Conley J.D., Viola R.E. L-Aspartase from Escherichia coli: substrate specificity and role of divalent metal ions. Biochemistry. 27:1988;9089-9093.
    • (1988) Biochemistry , vol.27 , pp. 9089-9093
    • Falzone, C.J.1    Karsten, W.E.2    Conley, J.D.3    Viola, R.E.4
  • 37
    • 0017881332 scopus 로고
    • The α-helix dipole and properties of proteins
    • Hol W.G.J., van Duijnen P.T., Berendsen H.J.C. The α-helix dipole and properties of proteins. Nature. 273:1978;443-446.
    • (1978) Nature , vol.273 , pp. 443-446
    • Hol, W.G.J.1    Van Duijnen, P.T.2    Berendsen, H.J.C.3
  • 38
    • 0000024872 scopus 로고
    • The temperature dependence of the steady state kinetic parameters of the fumarase reaction
    • Brant D.A., Barnett L.B., Alberty R.A. The temperature dependence of the steady state kinetic parameters of the fumarase reaction. J. Am. Chem. Soc. 85:1963;2204-2209.
    • (1963) J. Am. Chem. Soc. , vol.85 , pp. 2204-2209
    • Brant, D.A.1    Barnett, L.B.2    Alberty, R.A.3
  • 39
    • 0025720599 scopus 로고
    • Expression of duck lens δ-crystallin cDNAs in yeast and bacterial hosts. δ2-Crystallin is an active arginionosuccinate lyase
    • Barbosa P., Wistow G.J., Cialkowski M., Piatigorsky J., O'Brien W.E. Expression of duck lens δ-crystallin cDNAs in yeast and bacterial hosts. δ2-Crystallin is an active arginionosuccinate lyase. J. Biol. Chem. 266:1991;22319-22322.
    • (1991) J. Biol. Chem. , vol.266 , pp. 22319-22322
    • Barbosa, P.1    Wistow, G.J.2    Cialkowski, M.3    Piatigorsky, J.4    O'Brien, W.E.5
  • 40
    • 0035814902 scopus 로고    scopus 로고
    • Structural studies of duck δ1 and δ2 crystallin suggest conformational changes occur during catalysis
    • Sampaleanu L.M., Vallée F., Slingsby C., Howell P.L. Structural studies of duck δ1 and δ2 crystallin suggest conformational changes occur during catalysis. Biochemistry. 40:2001;2732-2742.
    • (2001) Biochemistry , vol.40 , pp. 2732-2742
    • Sampaleanu, L.M.1    Vallée, F.2    Slingsby, C.3    Howell, P.L.4
  • 41
    • 0033596716 scopus 로고    scopus 로고
    • Mutational analysis of amino acid residues involved in argininosuccinate lyase activity in duck δ II crystallin
    • Chakraborty A.R., Davidson A., Howell P.L. Mutational analysis of amino acid residues involved in argininosuccinate lyase activity in duck δ II crystallin. Biochemistry. 38:1999;2435-2443.
    • (1999) Biochemistry , vol.38 , pp. 2435-2443
    • Chakraborty, A.R.1    Davidson, A.2    Howell, P.L.3
  • 42
    • 0025166944 scopus 로고
    • Thermodynamics of industrially-important, enzyme-catalyzed reactions
    • Tewari Y.B. Thermodynamics of industrially-important, enzyme-catalyzed reactions. Appl. Biochem. Biotechnol. 23:1990;187-203.
    • (1990) Appl. Biochem. Biotechnol. , vol.23 , pp. 187-203
    • Tewari, Y.B.1
  • 43
    • 0034017055 scopus 로고    scopus 로고
    • Factors enhancing protein thermostability
    • Kumar S., Tsai C.-J., Nussinov R. Factors enhancing protein thermostability. Protein Eng. 13:2000;179-191.
    • (2000) Protein Eng. , vol.13 , pp. 179-191
    • Kumar, S.1    Tsai, C.-J.2    Nussinov, R.3
  • 44
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 45
    • 0001455061 scopus 로고
    • Weissenberg camera for macromolecules with imaging plate data collection system at the Photon Factory: Present status and future plan
    • Sakabe N., Ikemizu S., Sakabe K., Higashi T., Nakagawa A., Watanabe N., et al. Weissenberg camera for macromolecules with imaging plate data collection system at the Photon Factory: present status and future plan. Rev. Sci. Instrum. 66:1995;1276-1281.
    • (1995) Rev. Sci. Instrum. , vol.66 , pp. 1276-1281
    • Sakabe, N.1    Ikemizu, S.2    Sakabe, K.3    Higashi, T.4    Nakagawa, A.5    Watanabe, N.6
  • 46
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 47
    • 84920325457 scopus 로고
    • AMoRe: An automated package for molecular replacement
    • Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallog. sect. A. 50:1994;157-163.
    • (1994) Acta Crystallog. sect. A , vol.50 , pp. 157-163
    • Navaza, J.1
  • 52
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald I.K., Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238:1994;777-793.
    • (1994) J. Mol. Biol. , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 53
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D. 50:1994;760-763.
    • (1994) Acta Crystallog. sect. D , vol.50 , pp. 760-763
  • 54
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls A., Sharp K.A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11:1991;281-296.
    • (1991) Proteins: Struct. Funct. Genet. , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 55
    • 0030729838 scopus 로고    scopus 로고
    • An extensively modified version of MolScript that includes greatly enhanced coloring capabilities
    • Esnouf R.M. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J. Mol. Graph. Model. 15:1997;132-134.
    • (1997) J. Mol. Graph. Model. , vol.15 , pp. 132-134
    • Esnouf, R.M.1
  • 56
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: Photorealistic molecular graphics
    • Merritt E.A., Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524.
    • (1997) Methods Enzymol. , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2
  • 57
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.