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Volumn 337, Issue 2, 2004, Pages 399-416

Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism

Author keywords

Creatine; Creatininase; Creatinine; MAD, multiwavelength anomalous diffraction; PDB, protein data bank; SIRAS, single isomorphous replacement with anomalous scattering; X ray crystallography

Indexed keywords

AMIDASE; ASPARTIC ACID; CREATINE; CREATININASE; GLUTAMIC ACID; HISTIDINE; MANGANESE; ZINC;

EID: 1442299234     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.01.022     Document Type: Article
Times cited : (21)

References (42)
  • 1
    • 0017170403 scopus 로고
    • Creatinine decomposing enzymes in Pseudomonas putida
    • Tsuru D., Oka I., Yoshimoto T. Creatinine decomposing enzymes in Pseudomonas putida. Agric. Biol. Chem. 40:1976;1011-1018.
    • (1976) Agric. Biol. Chem. , vol.40 , pp. 1011-1018
    • Tsuru, D.1    Oka, I.2    Yoshimoto, T.3
  • 2
    • 0017048793 scopus 로고
    • Creatine amidinohydrolase of Pseudomonas putida: Crystallization and some properties
    • Yoshimoto T., Oka I., Tsuru D. Creatine amidinohydrolase of Pseudomonas putida: crystallization and some properties. Arch. Biochem. Biophys. 177:1976;508-515.
    • (1976) Arch. Biochem. Biophys. , vol.177 , pp. 508-515
    • Yoshimoto, T.1    Oka, I.2    Tsuru, D.3
  • 3
    • 0012009523 scopus 로고
    • Sarcosine dehydrogenase from Pseudomonas putida: Purification and some properties
    • Oka I., Yoshimoto T., Rikitake K., Ogushi S., Tsuru D. Sarcosine dehydrogenase from Pseudomonas putida: purification and some properties. Agric. Biol. Chem. 43:1979;1197-1203.
    • (1979) Agric. Biol. Chem. , vol.43 , pp. 1197-1203
    • Oka, I.1    Yoshimoto, T.2    Rikitake, K.3    Ogushi, S.4    Tsuru, D.5
  • 4
    • 0018367972 scopus 로고
    • Formaldehyde dehydrogenase from Pseudomonas putida: Purification and some properties
    • Ando M., Yoshimoto T., Ogushi S., Rikitake K., Shibata S., Tsuru D. Formaldehyde dehydrogenase from Pseudomonas putida: purification and some properties. J. Biochem. 85:1979;1165-1172.
    • (1979) J. Biochem. , vol.85 , pp. 1165-1172
    • Ando, M.1    Yoshimoto, T.2    Ogushi, S.3    Rikitake, K.4    Shibata, S.5    Tsuru, D.6
  • 5
    • 0018595232 scopus 로고
    • Creatinine amidohydrolase (creatininase) from Pseudomonas putida: Purification and some properties
    • Rikitake K., Oka I., Ando M., Yoshimoto T., Tsuru D. Creatinine amidohydrolase (creatininase) from Pseudomonas putida: purification and some properties. J. Biochem. 86:1979;1109-1117.
    • (1979) J. Biochem. , vol.86 , pp. 1109-1117
    • Rikitake, K.1    Oka, I.2    Ando, M.3    Yoshimoto, T.4    Tsuru, D.5
  • 6
    • 0029339608 scopus 로고
    • Cloning of the creatinine amidohydrolase gene from Pseudomonas sp. PS-7
    • Yamamoto K., Oka M., Kikuchi T., Emi S. Cloning of the creatinine amidohydrolase gene from Pseudomonas sp. PS-7. Biosci. Biotech. Biochem. 59:1995;1331-1332.
    • (1995) Biosci. Biotech. Biochem. , vol.59 , pp. 1331-1332
    • Yamamoto, K.1    Oka, M.2    Kikuchi, T.3    Emi, S.4
  • 7
    • 0011981668 scopus 로고    scopus 로고
    • Characterization and structural prediction of the Arthrobacter creatininase
    • Nishiya Y., Toda A., Oka M. Characterization and structural prediction of the Arthrobacter creatininase. J. Anal. Biol. Sci. 24:2001;144-149.
    • (2001) J. Anal. Biol. Sci. , vol.24 , pp. 144-149
    • Nishiya, Y.1    Toda, A.2    Oka, M.3
  • 8
    • 0031960956 scopus 로고    scopus 로고
    • Gene cluster for creatinine degradation in Arthrobacter sp. TE1826
    • Nishiya Y., Toda A., Imanaka T. Gene cluster for creatinine degradation in Arthrobacter sp. TE1826. Mol. Gen. Genet. 257:2001;581-586.
    • (2001) Mol. Gen. Genet. , vol.257 , pp. 581-586
    • Nishiya, Y.1    Toda, A.2    Imanaka, T.3
  • 9
    • 0024293450 scopus 로고
    • Crystal structure determination, refinement and molecular model of creatine amidinohydrolase from Pseudomonas putida
    • Hoeffken H.W., Knof S.H., Bartlett P.A., Huber R., Moellering H., Schumacher G. Crystal structure determination, refinement and molecular model of creatine amidinohydrolase from Pseudomonas putida. J. Mol. Biol. 204:1988;417-433.
    • (1988) J. Mol. Biol. , vol.204 , pp. 417-433
    • Hoeffken, H.W.1    Knof, S.H.2    Bartlett, P.A.3    Huber, R.4    Moellering, H.5    Schumacher, G.6
  • 10
    • 0025151091 scopus 로고
    • Enzymatic mechanism of creatine amidinohydrolase as deduced from crystal structures
    • Coll M., Knof S.H., Ohga Y., Messerschmidt A., Huber R., Mollering H., et al. Enzymatic mechanism of creatine amidinohydrolase as deduced from crystal structures. J. Mol. Biol. 214:1990;597-610.
    • (1990) J. Mol. Biol. , vol.214 , pp. 597-610
    • Coll, M.1    Knof, S.H.2    Ohga, Y.3    Messerschmidt, A.4    Huber, R.5    Mollering, H.6
  • 11
    • 0034254540 scopus 로고    scopus 로고
    • Monomeric sarcosine oxidase: Flavin reactivity and active site binding determinants
    • Wagner M.A., Trickey P., Chen Z.W., Mathews F.S., Jorns M.S. Monomeric sarcosine oxidase: flavin reactivity and active site binding determinants. Biochemistry. 39:2000;8813-8824.
    • (2000) Biochemistry , vol.39 , pp. 8813-8824
    • Wagner, M.A.1    Trickey, P.2    Chen, Z.W.3    Mathews, F.S.4    Jorns, M.S.5
  • 12
    • 0037031276 scopus 로고    scopus 로고
    • Monomeric sarcosine oxidase: Role of histidine 269 in catalysis
    • Zhao G., Song H., Chen Z.W., Mathews F.S., Jorns M.S. Monomeric sarcosine oxidase: role of histidine 269 in catalysis. Biochemistry. 41:2002;9751-9764.
    • (2002) Biochemistry , vol.41 , pp. 9751-9764
    • Zhao, G.1    Song, H.2    Chen, Z.W.3    Mathews, F.S.4    Jorns, M.S.5
  • 13
    • 0036445426 scopus 로고    scopus 로고
    • Crystal structure of formaldehyde dehydrogenase from Pseudomonas putida: The structural origin of the tightly bound cofactor in nicotinoprotein dehydrogenases
    • Tanaka N., Kusakabe Y., Ito K., Yoshimoto T., Nakamura K.T. Crystal structure of formaldehyde dehydrogenase from Pseudomonas putida: the structural origin of the tightly bound cofactor in nicotinoprotein dehydrogenases. J. Mol. Biol. 324:2002;519-533.
    • (2002) J. Mol. Biol. , vol.324 , pp. 519-533
    • Tanaka, N.1    Kusakabe, Y.2    Ito, K.3    Yoshimoto, T.4    Nakamura, K.T.5
  • 15
    • 0042736371 scopus 로고    scopus 로고
    • Crystal structure of creatininase from Pseudomonas putida: A novel fold and a case of convergent evolution
    • Beuth B., Niefind K., Schomburg D. Crystal structure of creatininase from Pseudomonas putida: a novel fold and a case of convergent evolution. J. Mol. Biol. 332:2003;287-301.
    • (2003) J. Mol. Biol. , vol.332 , pp. 287-301
    • Beuth, B.1    Niefind, K.2    Schomburg, D.3
  • 17
    • 0035912842 scopus 로고    scopus 로고
    • Molecular structure of dihydroorotase: A paradigm for catalysis through the use of a binuclear metal center
    • Thoden J.B., Phillips G.N., Neal T.M., Raushel F.M., Holden H.M. Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center. Biochemistry. 40:2001;6989-6997.
    • (2001) Biochemistry , vol.40 , pp. 6989-6997
    • Thoden, J.B.1    Phillips, G.N.2    Neal, T.M.3    Raushel, F.M.4    Holden, H.M.5
  • 18
    • 0036299882 scopus 로고    scopus 로고
    • X-ray structure of a dihydropyrimidinase from Thermus sp. at 1.3 Å resolution
    • Abendroth J., Niefind K., Schomburg D.X. X-ray structure of a dihydropyrimidinase from Thermus sp. at 1.3 Å resolution. J. Mol. Biol. 320:2002;143-156.
    • (2002) J. Mol. Biol. , vol.320 , pp. 143-156
    • Abendroth, J.1    Niefind, K.2    Schomburg, D.X.3
  • 19
    • 0037046968 scopus 로고    scopus 로고
    • The structure of L-hydantoinase from Arthrobacter aurescens leads to an understanding of dihydropyrimidinase substrate and enantio specificity
    • Abendroth J., Niefind K., May O., Siemann M., Syldatk C., Schomburg D. The structure of L-hydantoinase from Arthrobacter aurescens leads to an understanding of dihydropyrimidinase substrate and enantio specificity. Biochemistry. 41:2002;8589-8597.
    • (2002) Biochemistry , vol.41 , pp. 8589-8597
    • Abendroth, J.1    Niefind, K.2    May, O.3    Siemann, M.4    Syldatk, C.5    Schomburg, D.6
  • 20
    • 0037199453 scopus 로고    scopus 로고
    • Crystal structure of D-hydantoinase from Bacillus stearothermophilus: Insight into the stereochemistry of enantioselectivity
    • Cheon Y.H., Kim H.K., Han K.H., Abendroth J., Niefind K., Schomburg D., et al. Crystal structure of D-hydantoinase from Bacillus stearothermophilus: insight into the stereochemistry of enantioselectivity. Biochemistry. 41:2002;9410-9417.
    • (2002) Biochemistry , vol.41 , pp. 9410-9417
    • Cheon, Y.H.1    Kim, H.K.2    Han, K.H.3    Abendroth, J.4    Niefind, K.5    Schomburg, D.6
  • 21
    • 0026016867 scopus 로고
    • Refined crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.0 Å resolution
    • Herzberg O. Refined crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.0 Å resolution. J. Mol. Biol. 217:1991;701-719.
    • (1991) J. Mol. Biol. , vol.217 , pp. 701-719
    • Herzberg, O.1
  • 22
    • 0034479757 scopus 로고    scopus 로고
    • TOP: A new method for protein structure comparison and similarity searches
    • Lu G. TOP: a new method for protein structure comparison and similarity searches. J. Appl. Crystallog. 33:2000;176-183.
    • (2000) J. Appl. Crystallog. , vol.33 , pp. 176-183
    • Lu, G.1
  • 23
    • 0028889561 scopus 로고
    • Two-metal ion mechanism of bovine lens leucine aminopeptidase: Active site solvent structure and binding mode of L-leucinal, a gem-diolate transition state analogue, by X-ray crystallography
    • Strater N., Lipscomb W.N. Two-metal ion mechanism of bovine lens leucine aminopeptidase: active site solvent structure and binding mode of L-leucinal, a gem-diolate transition state analogue, by X-ray crystallography. Biochemistry. 34:1995;14792-14800.
    • (1995) Biochemistry , vol.34 , pp. 14792-14800
    • Strater, N.1    Lipscomb, W.N.2
  • 24
    • 0344931801 scopus 로고    scopus 로고
    • X-ray structure of aminopeptidase a from Escherichia coli and a model for the nucleoprotein complex in Xer site-specific recombination
    • Strater N., Sherratt D.J., Colloms S.D. X-ray structure of aminopeptidase A from Escherichia coli and a model for the nucleoprotein complex in Xer site-specific recombination. EMBO J. 18:1999;4513-4522.
    • (1999) EMBO J. , vol.18 , pp. 4513-4522
    • Strater, N.1    Sherratt, D.J.2    Colloms, S.D.3
  • 25
    • 0027160549 scopus 로고
    • Differentiation and identification of the two catalytic metal binding sites in bovine lens leucine aminopeptidase by X-ray crystallography
    • Kim H., Lipscomb W.N. Differentiation and identification of the two catalytic metal binding sites in bovine lens leucine aminopeptidase by X-ray crystallography. Proc. Natl Acad. Sci. USA. 90:1993;5006-5010.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 5006-5010
    • Kim, H.1    Lipscomb, W.N.2
  • 26
    • 0038671973 scopus 로고    scopus 로고
    • High-resolution X-ray structure of isoaspartyl dipeptidase from Escherichia coli
    • Thoden J.B., Marti-Arbona R., Raushel F.M., Holden H.M. High-resolution X-ray structure of isoaspartyl dipeptidase from Escherichia coli. Biochemistry. 42:2003;4874-4882.
    • (2003) Biochemistry , vol.42 , pp. 4874-4882
    • Thoden, J.B.1    Marti-Arbona, R.2    Raushel, F.M.3    Holden, H.M.4
  • 28
    • 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
  • 29
    • 0035844693 scopus 로고    scopus 로고
    • Enhancement of the thermal stability of pyroglutamyl peptidase I by introduction of an intersubunit disulfide bond
    • Kabashima T., Li Y., Kanada N., Ito K., Yoshimoto T. Enhancement of the thermal stability of pyroglutamyl peptidase I by introduction of an intersubunit disulfide bond. Biochim. Biophys. Acta. 1547:2001;214-220.
    • (2001) Biochim. Biophys. Acta , vol.1547 , pp. 214-220
    • Kabashima, T.1    Li, Y.2    Kanada, N.3    Ito, K.4    Yoshimoto, T.5
  • 30
    • 0031591389 scopus 로고    scopus 로고
    • The refined crystal structure of Bacillus cereus oligo-1,6-glucosidase at 2.0 Å resolution: Structural characterization of proline-substitution sites for protein thermostabilization
    • Watanabe K., Hata Y., Kizaki H., Katsube Y., Suzuki Y. The refined crystal structure of Bacillus cereus oligo-1,6-glucosidase at 2.0 Å resolution: structural characterization of proline-substitution sites for protein thermostabilization. J. Mol. Biol. 269:1997;142-153.
    • (1997) J. Mol. Biol. , vol.269 , pp. 142-153
    • Watanabe, K.1    Hata, Y.2    Kizaki, H.3    Katsube, Y.4    Suzuki, Y.5
  • 31
    • 0014432781 scopus 로고
    • Solvent content of protein crystals
    • Matthews B.W. Solvent content of protein crystals. J. Mol. Biol. 33:1968;491-497.
    • (1968) J. Mol. Biol. , vol.33 , pp. 491-497
    • Matthews, B.W.1
  • 33
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. D. 50:1994;760-763.
    • (1994) Acta Crystallog. D , vol.50 , pp. 760-763
  • 35
    • 0002634621 scopus 로고
    • Maximum likelihood refinement of heavy atom parameters
    • W. Wolf, P.R. Evans, & A.G.W. Leslie. Warrington, UK: Science and Engineering Research Council
    • Otwinowski W. Maximum likelihood refinement of heavy atom parameters. Wolf W., Evans P.R., Leslie A.G.W. Isomorphous replacement and anomalous scattering. 1991;80-86 Science and Engineering Research Council, Warrington, UK.
    • (1991) Isomorphous Replacement and Anomalous Scattering , pp. 80-86
    • Otwinowski, W.1
  • 37
    • 0032790081 scopus 로고    scopus 로고
    • XtalView/Xfit: A versatile program for manipulating atomic coordinates and electron density
    • McRee D.E. XtalView/Xfit: a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125:1999;156-165.
    • (1999) J. Struct. Biol. , vol.125 , pp. 156-165
    • McRee, D.E.1
  • 38
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov G.N., Vagin A.A., Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. D. 53:1997;240-255.
    • (1997) Acta Crystallog. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 39
    • 0000127585 scopus 로고
    • Automated refinement of protein models
    • Lamzin V.S., Wilson K.S. Automated refinement of protein models. Acta Crystallog. D. 49:1993;129-147.
    • (1993) Acta Crystallog. D , vol.49 , pp. 129-147
    • Lamzin, V.S.1    Wilson, K.S.2
  • 40
  • 41
    • 0031045818 scopus 로고    scopus 로고
    • Treatment of multiwavelength anomalous diffraction data as a special case of multiple isomorphous replacement
    • Ramakrishnan V., Biou V. Treatment of multiwavelength anomalous diffraction data as a special case of multiple isomorphous replacement. Methods Enzymol. 276:1997;538-557.
    • (1997) Methods Enzymol. , vol.276 , pp. 538-557
    • Ramakrishnan, V.1    Biou, V.2
  • 42
    • 0028057108 scopus 로고
    • Raster 3D version 2.0: A program for photorealistic molecular graphics
    • Merritt E.A., Murphy E.P. Raster 3D version 2.0: a program for photorealistic molecular graphics. Acta Crystallog. D. 50:1994;869-873.
    • (1994) Acta Crystallog. D , vol.50 , pp. 869-873
    • Merritt, E.A.1    Murphy, E.P.2


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