메뉴 건너뛰기




Volumn 1784, Issue 4, 2008, Pages 582-590

Modeling and experimental analyses reveal a two-domain structure and amino acids important for the activity of aminoglycoside resistance methyltransferase Sgm

Author keywords

Antibiotic resistance; Methylation; Modeling; Site directed mutagenesis

Indexed keywords

AMINO ACID; ENZYME SGM; KANAMYCIN; METHYLTRANSFERASE; UNCLASSIFIED DRUG;

EID: 40749086775     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2007.09.009     Document Type: Article
Times cited : (19)

References (59)
  • 1
    • 14844348264 scopus 로고    scopus 로고
    • Molecular insights into aminoglycoside action and resistance
    • Magnet S., and Blanchard J.S. Molecular insights into aminoglycoside action and resistance. Chem. Rev. 105 (2005) 477-498
    • (2005) Chem. Rev. , vol.105 , pp. 477-498
    • Magnet, S.1    Blanchard, J.S.2
  • 2
    • 0027478123 scopus 로고
    • Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes
    • Shaw K.J., Rather P.N., Hare R.S., and Miller G.H. Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes. Microbiol. Rev. 57 (1993) 138-163
    • (1993) Microbiol. Rev. , vol.57 , pp. 138-163
    • Shaw, K.J.1    Rather, P.N.2    Hare, R.S.3    Miller, G.H.4
  • 3
    • 0024459873 scopus 로고
    • How antibiotic-producing organisms avoid suicide
    • Cundliffe E. How antibiotic-producing organisms avoid suicide. Annu. Rev. Microbiol. 43 (1989) 207-233
    • (1989) Annu. Rev. Microbiol. , vol.43 , pp. 207-233
    • Cundliffe, E.1
  • 4
    • 0023091436 scopus 로고
    • Sites of action of two ribosomal RNA methylases responsible for resistance to aminoglycosides
    • Beauclerk A.A., and Cundliffe E. Sites of action of two ribosomal RNA methylases responsible for resistance to aminoglycosides. J. Mol. Biol. 193 (1987) 661-671
    • (1987) J. Mol. Biol. , vol.193 , pp. 661-671
    • Beauclerk, A.A.1    Cundliffe, E.2
  • 5
    • 0027159085 scopus 로고
    • Analysis of the nucleotide sequence of fmrT encoding the self-defense gene of the istamycin producer, Streptomyces tenjimariensis ATCC 31602; comparison with the sequences of kamB of Streptomyces tenebrarius NCIB 11028 and kamC of Saccharopolyspora hirsuta CL102
    • Ohta T., and Hasegawa M. Analysis of the nucleotide sequence of fmrT encoding the self-defense gene of the istamycin producer, Streptomyces tenjimariensis ATCC 31602; comparison with the sequences of kamB of Streptomyces tenebrarius NCIB 11028 and kamC of Saccharopolyspora hirsuta CL102. J. Antibiot. (Tokyo) 46 (1993) 511-517
    • (1993) J. Antibiot. (Tokyo) , vol.46 , pp. 511-517
    • Ohta, T.1    Hasegawa, M.2
  • 7
    • 0019878044 scopus 로고
    • Characterization of a plasmid-specified ribosome methylase associated with macrolide resistance
    • Shivakumar A.G., and Dubnau D. Characterization of a plasmid-specified ribosome methylase associated with macrolide resistance. Nucleic Acids Res. 9 (1981) 2549-2562
    • (1981) Nucleic Acids Res. , vol.9 , pp. 2549-2562
    • Shivakumar, A.G.1    Dubnau, D.2
  • 10
    • 12344305260 scopus 로고    scopus 로고
    • Plasmid-mediated 16S rRNA methylases conferring high-level aminoglycoside resistance in Escherichia coli and Klebsiella pneumoniae isolates from two Taiwanese hospitals
    • Yan J.J., Wu J.J., Ko W.C., Tsai S.H., Chuang C.L., Wu H.M., Lu Y.J., and Li J.D. Plasmid-mediated 16S rRNA methylases conferring high-level aminoglycoside resistance in Escherichia coli and Klebsiella pneumoniae isolates from two Taiwanese hospitals. J. Antimicrob. Chemother. 54 (2004) 1007-1012
    • (2004) J. Antimicrob. Chemother. , vol.54 , pp. 1007-1012
    • Yan, J.J.1    Wu, J.J.2    Ko, W.C.3    Tsai, S.H.4    Chuang, C.L.5    Wu, H.M.6    Lu, Y.J.7    Li, J.D.8
  • 11
    • 29944441901 scopus 로고    scopus 로고
    • Novel plasmid-mediated 16S rRNA methylase, RmtC, found in a Proteus mirabilis isolate demonstrating extraordinary high-level resistance against various aminoglycosides
    • Wachino J., Yamane K., Shibayama K., Kurokawa H., Shibata N., Suzuki S., Doi Y., Kimura K., Ike Y., and Arakawa Y. Novel plasmid-mediated 16S rRNA methylase, RmtC, found in a Proteus mirabilis isolate demonstrating extraordinary high-level resistance against various aminoglycosides. Antimicrob. Agents Chemother. 50 (2006) 178-184
    • (2006) Antimicrob. Agents Chemother. , vol.50 , pp. 178-184
    • Wachino, J.1    Yamane, K.2    Shibayama, K.3    Kurokawa, H.4    Shibata, N.5    Suzuki, S.6    Doi, Y.7    Kimura, K.8    Ike, Y.9    Arakawa, Y.10
  • 13
    • 0028589625 scopus 로고
    • Antimicrobial activity of arbekacin, a new aminoglycoside antibiotic, against methicillin-resistant Staphylococcus aureus
    • Inoue M., Nonoyama M., Okamoto R., and Ida T. Antimicrobial activity of arbekacin, a new aminoglycoside antibiotic, against methicillin-resistant Staphylococcus aureus. Drugs Exp. Clin. Res. 20 (1994) 233-239
    • (1994) Drugs Exp. Clin. Res. , vol.20 , pp. 233-239
    • Inoue, M.1    Nonoyama, M.2    Okamoto, R.3    Ida, T.4
  • 14
    • 0037303518 scopus 로고    scopus 로고
    • Macrolide antibiotic interaction and resistance on the bacterial ribosome
    • Poehlsgaard J., and Douthwaite S. Macrolide antibiotic interaction and resistance on the bacterial ribosome. Curr. Opin. Investig. Drugs 4 (2003) 140-148
    • (2003) Curr. Opin. Investig. Drugs , vol.4 , pp. 140-148
    • Poehlsgaard, J.1    Douthwaite, S.2
  • 16
    • 33646201327 scopus 로고    scopus 로고
    • Aminoglycoside resistance by ArmA-mediated ribosomal 16S methylation in human bacterial pathogens
    • Liou G.F., Yoshizawa S., Courvalin P., and Galimand M. Aminoglycoside resistance by ArmA-mediated ribosomal 16S methylation in human bacterial pathogens. J. Mol. Biol. 359 (2006) 358-364
    • (2006) J. Mol. Biol. , vol.359 , pp. 358-364
    • Liou, G.F.1    Yoshizawa, S.2    Courvalin, P.3    Galimand, M.4
  • 17
    • 0002898195 scopus 로고
    • Antibacterial susceptibility tests: dilution and disk diffusion methods
    • Murray P.R. (Ed), ASM Press, Washington DC
    • Wood G.L., and Washington J.A. Antibacterial susceptibility tests: dilution and disk diffusion methods. In: Murray P.R. (Ed). Manual of Clinical Microbiology (1995), ASM Press, Washington DC 1327-1341
    • (1995) Manual of Clinical Microbiology , pp. 1327-1341
    • Wood, G.L.1    Washington, J.A.2
  • 19
    • 33750001271 scopus 로고    scopus 로고
    • MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information
    • Pei J., and Grishin N.V. MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res. 34 (2006) 4364-4374
    • (2006) Nucleic Acids Res. , vol.34 , pp. 4364-4374
    • Pei, J.1    Grishin, N.V.2
  • 20
    • 0043123216 scopus 로고    scopus 로고
    • GeneSilico protein structure prediction meta-server
    • Kurowski M.A., and Bujnicki J.M. GeneSilico protein structure prediction meta-server. Nucleic Acids Res. 31 (2003) 3305-3307
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3305-3307
    • Kurowski, M.A.1    Bujnicki, J.M.2
  • 21
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292 (1999) 195-202
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 23
    • 0033933636 scopus 로고    scopus 로고
    • Cascaded multiple classifiers for secondary structure prediction
    • Ouali M., and King R.D. Cascaded multiple classifiers for secondary structure prediction. Protein Sci. 9 (2000) 1162-1176
    • (2000) Protein Sci. , vol.9 , pp. 1162-1176
    • Ouali, M.1    King, R.D.2
  • 24
    • 17844392864 scopus 로고    scopus 로고
    • Combining prediction of secondary structure and solvent accessibility in proteins
    • Adamczak R., Porollo A., and Meller J. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins 59 (2005) 467-475
    • (2005) Proteins , vol.59 , pp. 467-475
    • Adamczak, R.1    Porollo, A.2    Meller, J.3
  • 25
    • 0142027795 scopus 로고    scopus 로고
    • Coupled prediction of protein secondary and tertiary structure
    • Meiler J., and Baker D. Coupled prediction of protein secondary and tertiary structure. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 12105-12110
    • (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , pp. 12105-12110
    • Meiler, J.1    Baker, D.2
  • 26
    • 17444397116 scopus 로고    scopus 로고
    • Porter: a new, accurate server for protein secondary structure prediction
    • Pollastri G., and McLysaght A. Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics 21 (2005) 1719-1720
    • (2005) Bioinformatics , vol.21 , pp. 1719-1720
    • Pollastri, G.1    McLysaght, A.2
  • 27
    • 23144465987 scopus 로고    scopus 로고
    • SCRATCH: a protein structure and structural feature prediction server
    • Cheng J., Randall A.Z., Sweredoski M.J., and Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res. 33 (2005) W72-W76
    • (2005) Nucleic Acids Res. , vol.33
    • Cheng, J.1    Randall, A.Z.2    Sweredoski, M.J.3    Baldi, P.4
  • 28
    • 0242362161 scopus 로고    scopus 로고
    • Combining local-structure, fold-recognition, and new fold methods for protein structure prediction
    • Karplus K., Karchin R., Draper J., Casper J., Mandel-Gutfreund Y., Diekhans M., and Hughey R. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins 53 Suppl 6 (2003) 491-496
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 491-496
    • Karplus, K.1    Karchin, R.2    Draper, J.3    Casper, J.4    Mandel-Gutfreund, Y.5    Diekhans, M.6    Hughey, R.7
  • 29
    • 0034663597 scopus 로고    scopus 로고
    • Application of multiple sequence alignment profiles to improve protein secondary structure prediction
    • Cuff J.A., and Barton G.J. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 40 (2000) 502-511
    • (2000) Proteins , vol.40 , pp. 502-511
    • Cuff, J.A.1    Barton, G.J.2
  • 33
    • 33747868721 scopus 로고    scopus 로고
    • Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines
    • Vullo A., Bortolami O., Pollastri G., and Tosatto S.C. Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res. 34 (2006) W164-W168
    • (2006) Nucleic Acids Res. , vol.34
    • Vullo, A.1    Bortolami, O.2    Pollastri, G.3    Tosatto, S.C.4
  • 34
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (2005) 951-960
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 36
    • 1542609543 scopus 로고    scopus 로고
    • FORTE: a profile-profile comparison tool for protein fold recognition
    • Tomii K., and Akiyama Y. FORTE: a profile-profile comparison tool for protein fold recognition. Bioinformatics 20 (2004) 594-595
    • (2004) Bioinformatics , vol.20 , pp. 594-595
    • Tomii, K.1    Akiyama, Y.2
  • 37
    • 0034595501 scopus 로고    scopus 로고
    • Enhanced genome annotation using structural profiles in the program 3D-PSSM
    • Kelley L.A., MacCallum R.M., and Sternberg M.J. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299 (2000) 499-520
    • (2000) J. Mol. Biol. , vol.299 , pp. 499-520
    • Kelley, L.A.1    MacCallum, R.M.2    Sternberg, M.J.3
  • 38
    • 0033654768 scopus 로고    scopus 로고
    • Hybrid fold recognition: combining sequence derived properties with evolutionary information
    • Fischer D. Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pacific Symp. Biocomp. (2000) 119-130
    • (2000) Pacific Symp. Biocomp. , pp. 119-130
    • Fischer, D.1
  • 39
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • Shi J., Blundell T.L., and Mizuguchi K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310 (2001) 243-257
    • (2001) J. Mol. Biol. , vol.310 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 40
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences
    • Jones D.T. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287 (1999) 797-815
    • (1999) J. Mol. Biol. , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 41
    • 2542631929 scopus 로고    scopus 로고
    • Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition
    • Zhou H., and Zhou Y. Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 55 (2004) 1005-1013
    • (2004) Proteins , vol.55 , pp. 1005-1013
    • Zhou, H.1    Zhou, Y.2
  • 42
    • 0034780030 scopus 로고    scopus 로고
    • Pcons: a neural-network-based consensus predictor that improves fold recognition
    • Lundstrom J., Rychlewski L., Bujnicki J., and Elofsson A. Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci. 10 (2001) 2354-2362
    • (2001) Protein Sci. , vol.10 , pp. 2354-2362
    • Lundstrom, J.1    Rychlewski, L.2    Bujnicki, J.3    Elofsson, A.4
  • 43
    • 0242362160 scopus 로고    scopus 로고
    • A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation
    • Kosinski J., Cymerman I.A., Feder M., Kurowski M.A., Sasin J.M., and Bujnicki J.M. A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation. Proteins 53 Suppl 6 (2003) 369-379
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 369-379
    • Kosinski, J.1    Cymerman, I.A.2    Feder, M.3    Kurowski, M.A.4    Sasin, J.M.5    Bujnicki, J.M.6
  • 45
    • 0242330730 scopus 로고    scopus 로고
    • Assessment of homology-based predictions in CASP5
    • Tramontano A., and Morea V. Assessment of homology-based predictions in CASP5. Proteins 53 Suppl 6 (2003) 352-368
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 352-368
    • Tramontano, A.1    Morea, V.2
  • 46
    • 30344449457 scopus 로고    scopus 로고
    • Assessment of fold recognition predictions in CASP6
    • Wang G., Jin Y., and Dunbrack Jr. R.L. Assessment of fold recognition predictions in CASP6. Proteins 61 Suppl 7 (2005) 46-66
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 46-66
    • Wang, G.1    Jin, Y.2    Dunbrack Jr., R.L.3
  • 47
    • 0002401076 scopus 로고    scopus 로고
    • mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships
    • Bujnicki J.M., Feder M., Radlinska M., and Rychlewski L. mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships. BMC Bioinformatics 2 (2001) 2
    • (2001) BMC Bioinformatics , vol.2 , pp. 2
    • Bujnicki, J.M.1    Feder, M.2    Radlinska, M.3    Rychlewski, L.4
  • 48
    • 0012588361 scopus 로고    scopus 로고
    • RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited-bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure
    • Bujnicki J.M., and Rychlewski L. RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited-bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure. BMC Bioinformatics 3 (2002) 10
    • (2002) BMC Bioinformatics , vol.3 , pp. 10
    • Bujnicki, J.M.1    Rychlewski, L.2
  • 49
    • 17944373789 scopus 로고    scopus 로고
    • Sequence-structure-function relationships of a tRNA (m(7)G46) methyltransferase studied by homology modeling and site-directed mutagenesis
    • Purta E., van Vliet F., Tricot C., De Bie L.G., Feder M., Skowronek K., Droogmans L., and Bujnicki J.M. Sequence-structure-function relationships of a tRNA (m(7)G46) methyltransferase studied by homology modeling and site-directed mutagenesis. Proteins 59 (2005) 482-488
    • (2005) Proteins , vol.59 , pp. 482-488
    • Purta, E.1    van Vliet, F.2    Tricot, C.3    De Bie, L.G.4    Feder, M.5    Skowronek, K.6    Droogmans, L.7    Bujnicki, J.M.8
  • 50
    • 0037406141 scopus 로고    scopus 로고
    • Can correct protein models be identified?
    • Wallner B., and Elofsson A. Can correct protein models be identified?. Protein Sci. 12 (2003) 1073-1086
    • (2003) Protein Sci. , vol.12 , pp. 1073-1086
    • Wallner, B.1    Elofsson, A.2
  • 51
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons K.T., Kooperberg C., Huang E., and Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268 (1997) 209-225
    • (1997) J. Mol. Biol. , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 52
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker D., and Sali A. Protein structure prediction and structural genomics. Science 294 (2001) 93-96
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 53
    • 0033302662 scopus 로고    scopus 로고
    • Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation
    • Bujnicki J.M. Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation. In Silico Biol. 1 (1999) 175-182
    • (1999) In Silico Biol. , vol.1 , pp. 175-182
    • Bujnicki, J.M.1
  • 54
    • 27844530636 scopus 로고    scopus 로고
    • Natural history of S-adenosylmethionine-binding proteins
    • Kozbial P.Z., and Mushegian A.R. Natural history of S-adenosylmethionine-binding proteins. BMC Struct. Biol. 5 (2005) 19
    • (2005) BMC Struct. Biol. , vol.5 , pp. 19
    • Kozbial, P.Z.1    Mushegian, A.R.2
  • 55
    • 0142138438 scopus 로고    scopus 로고
    • Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions
    • Maravic G., Bujnicki J.M., Feder M., Pongor S., and Flogel M. Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions. Nucleic Acids Res. 31 (2003) 4941-4949
    • (2003) Nucleic Acids Res. , vol.31 , pp. 4941-4949
    • Maravic, G.1    Bujnicki, J.M.2    Feder, M.3    Pongor, S.4    Flogel, M.5
  • 56
    • 0042736455 scopus 로고    scopus 로고
    • Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'
    • Maravic G., Feder M., Pongor S., Flogel M., and Bujnicki J.M. Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'. J. Mol. Biol. 332 (2003) 99-109
    • (2003) J. Mol. Biol. , vol.332 , pp. 99-109
    • Maravic, G.1    Feder, M.2    Pongor, S.3    Flogel, M.4    Bujnicki, J.M.5
  • 57
    • 40749141658 scopus 로고    scopus 로고
    • Mutational analysis of the sgm gene from Micromonospora zionensis
    • Milojevic N., Kojic M., and Vasiljevic B. Mutational analysis of the sgm gene from Micromonospora zionensis. Arch. Biol. Sci. (Belgrade) 50 (1998) 151-158
    • (1998) Arch. Biol. Sci. (Belgrade) , vol.50 , pp. 151-158
    • Milojevic, N.1    Kojic, M.2    Vasiljevic, B.3
  • 58
    • 0032614298 scopus 로고    scopus 로고
    • Aminoglycoside phosphotransferases: proteins, structure, and mechanism
    • Wright G.D., and Thompson P.R. Aminoglycoside phosphotransferases: proteins, structure, and mechanism. Front. Biosci. 4 (1999) D9-D21
    • (1999) Front. Biosci. , vol.4
    • Wright, G.D.1    Thompson, P.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.