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Volumn 36, Issue 1, 1999, Pages 117-134

Conserved water molecules in a large family of microbial ribonucleases

Author keywords

Barnase; Hydration; Protein hydration; Ribonuclease; RNase T1

Indexed keywords

RIBONUCLEASE; WATER;

EID: 0033168566     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990701)36:1<117::AID-PROT10>3.0.CO;2-H     Document Type: Article
Times cited : (52)

References (52)
  • 1
    • 0020861687 scopus 로고
    • Water and proteins. II. The location and dynamics of water in protein systems and its relation to their stability and properties
    • Edsall JT, McKenzie HA. Water and proteins. II. The location and dynamics of water in protein systems and its relation to their stability and properties. Adv Biophys 1983;16:53-186.
    • (1983) Adv Biophys , vol.16 , pp. 53-186
    • Edsall, J.T.1    McKenzie, H.A.2
  • 2
    • 0026567907 scopus 로고
    • Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect
    • Eriksson AE, Baase WA, Zhang XJ et al. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 1992;255:178-183.
    • (1992) Science , vol.255 , pp. 178-183
    • Eriksson, A.E.1    Baase, W.A.2    Zhang, X.J.3
  • 3
    • 0029882171 scopus 로고    scopus 로고
    • Structural and energetic responses to cavity-creating mutations in hydrophobic cores: Observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities
    • Buckle AM, Cramer PK, Fersht AR. Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities. Biochemistry 1996;35:4298-4305.
    • (1996) Biochemistry , vol.35 , pp. 4298-4305
    • Buckle, A.M.1    Cramer, P.K.2    Fersht, A.R.3
  • 4
    • 0030045089 scopus 로고    scopus 로고
    • Structural and genetic analysis of the folding and function of T4 lysozyme
    • Matthews BW. Structural and genetic analysis of the folding and function of T4 lysozyme. FASEB J 1996;10:35-41.
    • (1996) FASEB J , vol.10 , pp. 35-41
    • Matthews, B.W.1
  • 5
    • 0343170500 scopus 로고
    • Dramatic thermostabilization of yeast iso-1-cytochrome c by an asparagine → leucine replacement at position 57
    • Das G, Hickey DR, McLendon D, McLendon G, Sherman F. Dramatic thermostabilization of yeast iso-1-cytochrome c by an asparagine → leucine replacement at position 57. Proc Natl Acad Sci USA 1989;86:496-499.
    • (1989) Proc Natl Acad Sci USA , vol.86 , pp. 496-499
    • Das, G.1    Hickey, D.R.2    McLendon, D.3    McLendon, G.4    Sherman, F.5
  • 6
    • 0026077448 scopus 로고
    • Enhanced thermodynamic stabilities of yeast Iso-1-cytochrome c with amino acid replacements at positions 52 and 102
    • Hickey DR, Berghuis AM, Lafond G, Jaefer JA, Cardillo TS, McLendon G. Enhanced thermodynamic stabilities of yeast Iso-1-cytochrome c with amino acid replacements at positions 52 and 102. J Biol Chem 1991;266:11686-11694.
    • (1991) J Biol Chem , vol.266 , pp. 11686-11694
    • Hickey, D.R.1    Berghuis, A.M.2    Lafond, G.3    Jaefer, J.A.4    Cardillo, T.S.5    McLendon, G.6
  • 8
    • 10544228949 scopus 로고    scopus 로고
    • The role of a conserved water molecule in the redox-dependent thermal stability of Iso-1-cytochrome c
    • Lett CM, Berghuis AM, Frey HE, Lepock JR, Guillemette JG. The role of a conserved water molecule in the redox-dependent thermal stability of Iso-1-cytochrome c. J Biol Chem 1996;271:29088-29093.
    • (1996) J Biol Chem , vol.271 , pp. 29088-29093
    • Lett, C.M.1    Berghuis, A.M.2    Frey, H.E.3    Lepock, J.R.4    Guillemette, J.G.5
  • 9
    • 0027164289 scopus 로고
    • Designed replacement of an internal hydration water molecule in BPTI: Structural and functional implications of a glycine-to-serine mutation
    • Berndt KD, Beunink J, Schroder W, Wuthrich K. Designed replacement of an internal hydration water molecule in BPTI: structural and functional implications of a glycine-to-serine mutation. Biochemistry 1993;32:4564-4570.
    • (1993) Biochemistry , vol.32 , pp. 4564-4570
    • Berndt, K.D.1    Beunink, J.2    Schroder, W.3    Wuthrich, K.4
  • 10
    • 0028168463 scopus 로고
    • Cavity mutants of savinase. Crystal structures and differential scanning calorimetry experiments give hints of the function of buried water molecules in subtilisins
    • Pedersen JT, Olsen OH, Betzel C, Eschenburg S, Branner S, Hastrup S. Cavity mutants of savinase. Crystal structures and differential scanning calorimetry experiments give hints of the function of buried water molecules in subtilisins. J Mol Biol 1994;242:193-202.
    • (1994) J Mol Biol , vol.242 , pp. 193-202
    • Pedersen, J.T.1    Olsen, O.H.2    Betzel, C.3    Eschenburg, S.4    Branner, S.5    Hastrup, S.6
  • 11
    • 0023051843 scopus 로고
    • Internal cavities and buried waters in globular proteins
    • Rashin AA, Iofin M, Honig B. Internal cavities and buried waters in globular proteins. Biochemistry 1986;25:3619-3625.
    • (1986) Biochemistry , vol.25 , pp. 3619-3625
    • Rashin, A.A.1    Iofin, M.2    Honig, B.3
  • 12
    • 0027082924 scopus 로고
    • Internal water molecules and H-bonding in biological macromolecules: A review of structural features with functional implications
    • Meyer E. Internal water molecules and H-bonding in biological macromolecules: a review of structural features with functional implications. Protein Sci 1992;1:1543-1562.
    • (1992) Protein Sci , vol.1 , pp. 1543-1562
    • Meyer, E.1
  • 13
    • 0028103082 scopus 로고
    • The active site of bovine pancreatic ribonuclease: An example of solvent modulated specificity
    • Gilliland GL, Dill J, Pechik I, Svensson LA, Sjolin L. The active site of bovine pancreatic ribonuclease: an example of solvent modulated specificity. Protein Pept Lett 1994;1:60-65.
    • (1994) Protein Pept Lett , vol.1 , pp. 60-65
    • Gilliland, G.L.1    Dill, J.2    Pechik, I.3    Svensson, L.A.4    Sjolin, L.5
  • 14
    • 0030466444 scopus 로고    scopus 로고
    • Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design
    • Ladbury JE. Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design. Chem Biol 1996;3:973-980.
    • (1996) Chem Biol , vol.3 , pp. 973-980
    • Ladbury, J.E.1
  • 15
    • 0000492269 scopus 로고    scopus 로고
    • Crystal structure of the peanut lectin - T-antigen complex. Carbohydrate specificity generated by water bridges
    • Ravishankar R, Ravindran M, Suguna K, Surolia A, Vijayan M. Crystal structure of the peanut lectin - T-antigen complex. Carbohydrate specificity generated by water bridges. Curr Sci 1997;72:855-861.
    • (1997) Curr Sci , vol.72 , pp. 855-861
    • Ravishankar, R.1    Ravindran, M.2    Suguna, K.3    Surolia, A.4    Vijayan, M.5
  • 16
    • 0031047683 scopus 로고    scopus 로고
    • The role of water in protein-DNA interactions
    • Schwabe JWR. The role of water in protein-DNA interactions. Curr Opin Struct Biol 1997;7:126-134.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 126-134
    • Schwabe, J.W.R.1
  • 17
    • 0030877826 scopus 로고    scopus 로고
    • A decade of protein engineering on ribonuclease T1: Atomic dissection of the enzyme-substrate interactions
    • Steyaert J. A decade of protein engineering on ribonuclease T1: Atomic dissection of the enzyme-substrate interactions. Eur J Biochem. 1997;247:1-11.
    • (1997) Eur J Biochem. , vol.247 , pp. 1-11
    • Steyaert, J.1
  • 18
    • 0025727187 scopus 로고
    • Structurally conserved water molecules in ribonuclease T1
    • Malin R, Zielenkiewicz P, Saenger W. Structurally conserved water molecules in ribonuclease T1. J Biol Chem 1991;266:4848-4852.
    • (1991) J Biol Chem , vol.266 , pp. 4848-4852
    • Malin, R.1    Zielenkiewicz, P.2    Saenger, W.3
  • 19
    • 0028331910 scopus 로고
    • Crystallographic study of Glu58Ala RNase T1*2'-guanosine monophosphate at 1.9 Å resolution
    • Pletinckx J, Steyaert J, Zegers I, Choe H-W, Heinemann U, Wyns L. Crystallographic study of Glu58Ala RNase T1*2'-guanosine monophosphate at 1.9 Å resolution. Biochemistry 1994;33:1654-1662.
    • (1994) Biochemistry , vol.33 , pp. 1654-1662
    • Pletinckx, J.1    Steyaert, J.2    Zegers, I.3    Choe, H.-W.4    Heinemann, U.5    Wyns, L.6
  • 20
    • 0032891093 scopus 로고    scopus 로고
    • Dissection of the structural and functional role of a conserved hydration site in RNase T1
    • Langhorst U, Loris R, Denisov VP et al. Dissection of the structural and functional role of a conserved hydration site in RNase T1. Protein Sci. 1999;8:722-730.
    • (1999) Protein Sci. , vol.8 , pp. 722-730
    • Langhorst, U.1    Loris, R.2    Denisov, V.P.3
  • 21
    • 0011887231 scopus 로고
    • Restrained least-squares refinement of the crystal structure of the ribonuclease T1-2'-guanylic acid complex at 1.9 Å resolution
    • Arm R, Heinemann U, Maslowska M, Tokuoka R, Saenger W. Restrained least-squares refinement of the crystal structure of the ribonuclease T1-2'-guanylic acid complex at 1.9 Å resolution. Acta Crystallogr B 1987;43:548-554.
    • (1987) Acta Crystallogr B , vol.43 , pp. 548-554
    • Arm, R.1    Heinemann, U.2    Maslowska, M.3    Tokuoka, R.4    Saenger, W.5
  • 22
    • 0024297213 scopus 로고
    • Three-dimensional structure of the Ribonuclease T1*2'GMP complex at 1.9 Å resolution
    • Arni R, Heinemann U, Tokuoka R, Saenger W. Three-dimensional structure of the Ribonuclease T1*2'GMP complex at 1.9 Å resolution. J Biol Chem 1988;263:15358-15368.
    • (1988) J Biol Chem , vol.263 , pp. 15358-15368
    • Arni, R.1    Heinemann, U.2    Tokuoka, R.3    Saenger, W.4
  • 23
    • 0027967768 scopus 로고
    • Conserved waters in legume lectin crystal structures
    • Loris R, Stas PPG, Wyns L. Conserved waters in legume lectin crystal structures. J Biol Chem 1994;269:26722-26733.
    • (1994) J Biol Chem , vol.269 , pp. 26722-26733
    • Loris, R.1    Stas, P.P.G.2    Wyns, L.3
  • 25
    • 0028564999 scopus 로고
    • The structures of RNase A complexed with 3'-CMP and d(CpA): Active site conformation and conserved water molecules
    • Zegers I, Maes D, Dao-Thi M, Poortmans F, Palmer R, Wyns L. The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules. Protein Sci 1994;3:2322-2339.
    • (1994) Protein Sci , vol.3 , pp. 2322-2339
    • Zegers, I.1    Maes, D.2    Dao-Thi, M.3    Poortmans, F.4    Palmer, R.5    Wyns, L.6
  • 26
    • 0028341789 scopus 로고
    • Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme
    • Zhang XJ, Matthews BW. Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme. Protein Sci 1994;3:1031-1039.
    • (1994) Protein Sci , vol.3 , pp. 1031-1039
    • Zhang, X.J.1    Matthews, B.W.2
  • 27
    • 0019944172 scopus 로고
    • Molecular structure of a new family of ribonucleases
    • Mauguen Y, Hartley RW, Dodson EJ et al. Molecular structure of a new family of ribonucleases. Nature 1982;297:162-164.
    • (1982) Nature , vol.297 , pp. 162-164
    • Mauguen, Y.1    Hartley, R.W.2    Dodson, E.J.3
  • 29
    • 0001629142 scopus 로고
    • The structural and sequence homology of a family of microbial ribonucleases
    • Hill C, Dodson G, Heinemann U et al. The structural and sequence homology of a family of microbial ribonucleases. Trends Biochem Sci 1983;8:364-369.
    • (1983) Trends Biochem Sci , vol.8 , pp. 364-369
    • Hill, C.1    Dodson, G.2    Heinemann, U.3
  • 30
    • 0025325256 scopus 로고
    • Comparison of active sites of some microbial RNases: Structural basis for guanylic specificity
    • Sevcik J, Sanishvili RG, Pavlovsky AG, Polyakov KM. Comparison of active sites of some microbial RNases: structural basis for guanylic specificity. Trends Biochem Sci 1990;15:158-162.
    • (1990) Trends Biochem Sci , vol.15 , pp. 158-162
    • Sevcik, J.1    Sanishvili, R.G.2    Pavlovsky, A.G.3    Polyakov, K.M.4
  • 31
    • 0000446384 scopus 로고
    • Determination and least-squares refinement of the structures of ribonuclease Sa and its complex with 3'guanylic acid at 1.8 Å resolution
    • Sevcik J, Dodson EJ, Dodson GG. Determination and least-squares refinement of the structures of ribonuclease Sa and its complex with 3'guanylic acid at 1.8 Å resolution. Acta Crystallogr B 1991;47:240-253.
    • (1991) Acta Crystallogr B , vol.47 , pp. 240-253
    • Sevcik, J.1    Dodson, E.J.2    Dodson, G.G.3
  • 32
    • 0013033198 scopus 로고
    • Water structure of crystallized proteins: High-resolution studies
    • Westhof E, editor. London: MacMillan Press
    • Frey M. Water structure of crystallized proteins: high-resolution studies. In: Westhof E, editor. Water and biological macromolecules. London: MacMillan Press; 1993. p 98-101.
    • (1993) Water and Biological Macromolecules , pp. 98-101
    • Frey, M.1
  • 33
    • 0025045326 scopus 로고
    • Histidine 40 of ribonuclease T1 acts as a base catalyst when the true catalytic base, glutamic acid 58, is replaced by alanine
    • Steyaert J, Hallenga K, Wyns L, Stanssens P. Histidine 40 of ribonuclease T1 acts as a base catalyst when the true catalytic base, glutamic acid 58, is replaced by alanine. Biochemistry 1990;29:9064-9072.
    • (1990) Biochemistry , vol.29 , pp. 9064-9072
    • Steyaert, J.1    Hallenga, K.2    Wyns, L.3    Stanssens, P.4
  • 34
    • 0027550008 scopus 로고
    • A purification method for labile variants of ribonuclease T1
    • Mayr LH, Schmid FX. A purification method for labile variants of ribonuclease T1. Protein Expr Purif 1993;4:52-58.
    • (1993) Protein Expr Purif , vol.4 , pp. 52-58
    • Mayr, L.H.1    Schmid, F.X.2
  • 35
    • 0031979619 scopus 로고    scopus 로고
    • Hydrolysis of a slow cyclic thiophosphate substrate of RNase T1 analyzed by time-resolved crystallography
    • Zegers I, Loris R, Dehollander G et al. Hydrolysis of a slow cyclic thiophosphate substrate of RNase T1 analyzed by time-resolved crystallography. Nat Struct Biol 1998;5:280-283.
    • (1998) Nat Struct Biol , vol.5 , pp. 280-283
    • Zegers, I.1    Loris, R.2    Dehollander, G.3
  • 36
    • 84920325457 scopus 로고
    • AMORE: An automated package for molecular replacement
    • Navaza J. AMORE: an automated package for molecular replacement. Acta Crystallogr A 1994;50:157-163.
    • (1994) Acta Crystallogr A , vol.50 , pp. 157-163
    • Navaza, J.1
  • 37
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum likelihood method
    • Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum likelihood method. Acta Crystallogr D 1997;53:240-255.
    • (1997) Acta Crystallogr D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 38
    • 0000127585 scopus 로고
    • Automated refinement of protein models
    • Lamzin VS, Wilson KS. Automated refinement of protein models. Acta Crystallogr D 1993;49:129-147.
    • (1993) Acta Crystallogr D , vol.49 , pp. 129-147
    • Lamzin, V.S.1    Wilson, K.S.2
  • 40
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D 1994;50: 760-763.
    • (1994) Acta Crystallogr D , vol.50 , pp. 760-763
  • 41
    • 0001334491 scopus 로고
    • Restrained structure-factor least-squares refinement of protein structures using a vector processing computer
    • Haneef I, Moss DS, Stanford MJ, Borkakoti N. Restrained structure-factor least-squares refinement of protein structures using a vector processing computer. Acta Crystallogr A 1985;41:426-433.
    • (1985) Acta Crystallogr A , vol.41 , pp. 426-433
    • Haneef, I.1    Moss, D.S.2    Stanford, M.J.3    Borkakoti, N.4
  • 42
    • 0000568418 scopus 로고
    • RESTRAIN: Restrained structure-factor least-squares refinement program for macromolecular structures
    • Driessen H, Haneef MIJ, Harris GW, Howlin B, Khan G, Moss DS. RESTRAIN: restrained structure-factor least-squares refinement program for macromolecular structures. J Appl Crystallogr 1989; 22:510-516.
    • (1989) J Appl Crystallogr , vol.22 , pp. 510-516
    • Driessen, H.1    Haneef, M.I.J.2    Harris, G.W.3    Howlin, B.4    Khan, G.5    Moss, D.S.6
  • 43
    • 0005696795 scopus 로고
    • Variance and covariance in experimental electron density studies, and the use of chemical equivalence
    • Rees DC. Variance and covariance in experimental electron density studies, and the use of chemical equivalence. Acta Crystallogr A 1979;32:483-488.
    • (1979) Acta Crystallogr A , vol.32 , pp. 483-488
    • Rees, D.C.1
  • 44
    • 0017411710 scopus 로고
    • The protein data bank: A computer-based archival file for macromolecular structures
    • Bernstein FC, Koetzle TF, Williams GJB et al. The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
    • (1977) J Mol Biol , vol.112 , pp. 535-542
    • Bernstein, F.C.1    Koetzle, T.F.2    Williams, G.J.B.3
  • 45
    • 0030039296 scopus 로고    scopus 로고
    • PROMOTIF - A program to identify and analyze structural motifs in proteins
    • Hutchinson EG, Thornton JM. PROMOTIF - a program to identify and analyze structural motifs in proteins. Protein Sci 1996;5:212-220.
    • (1996) Protein Sci , vol.5 , pp. 212-220
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 46
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 47
    • 0003742069 scopus 로고
    • London: Department of Biochemistry and Molecular Biology, University College London
    • Hubbard SJ, Thornton JM. "NACCESS", Computer Program. London: Department of Biochemistry and Molecular Biology, University College London; 1993.
    • (1993) "NACCESS", Computer Program
    • Hubbard, S.J.1    Thornton, J.M.2
  • 48
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971;55:397-400.
    • (1971) J Mol Biol , vol.55 , pp. 397-400
    • Lee, B.1    Richards, F.M.2
  • 49
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J Mol Biol 1994;238:777-793.
    • (1994) J Mol Biol , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 50
    • 0028154121 scopus 로고
    • Crystal structure of RNase T1 with 3'-guanylic acid and guanosine
    • Zegers I, Haikal AF, Palmer R, Wyns L. Crystal structure of RNase T1 with 3'-guanylic acid and guanosine J Biol Chem 1994;269:127-133.
    • (1994) J Biol Chem , vol.269 , pp. 127-133
    • Zegers, I.1    Haikal, A.F.2    Palmer, R.3    Wyns, L.4
  • 51
    • 0027133653 scopus 로고
    • Crystal structure analysis of mutations in the hydrophobic core of barnase
    • Buckle AM, Henrick K, Fersht AR. Crystal structure analysis of mutations in the hydrophobic core of barnase. J Mol Biol 1993;234: 847-860.
    • (1993) J Mol Biol , vol.234 , pp. 847-860
    • Buckle, A.M.1    Henrick, K.2    Fersht, A.R.3
  • 52
    • 0030729838 scopus 로고    scopus 로고
    • An extensively modified version of MolScript that includes greatly enhanced colouring capabilities
    • Esnouf RM. An extensively modified version of MolScript that includes greatly enhanced colouring capabilities. J Mol Graph Model 1997;15:132-134.
    • (1997) J Mol Graph Model , vol.15 , pp. 132-134
    • Esnouf, R.M.1


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