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Volumn 12, Issue 4, 2004, Pages 593-602

Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; BACTERIAL ENZYME; BACTERIAL RNA; GUANOSINE; METHYLTRANSFERASE; PHOSPHATE; PROTEIN SUBUNIT; S ADENOSYLMETHIONINE; TRANSFER RNA;

EID: 1842607227     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.03.003     Document Type: Article
Times cited : (107)

References (32)
  • 1
    • 0030038464 scopus 로고    scopus 로고
    • Methods used in the structure determination of bovine mitochondrial F1 ATPase
    • Abrahams J.P., Leslie A.G.W. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr. D. 52:1996;30-42.
    • (1996) Acta Crystallogr. D , vol.52 , pp. 30-42
    • Abrahams, J.P.1    Leslie, A.G.W.2
  • 3
    • 0036132209 scopus 로고    scopus 로고
    • Spout: A class of methyltransferases that includes spoU and trmD rna methylase superfamilies and novel superfamilies of predicted prokaryotic rna methylases
    • Anantharaman V., Koonin E.V., Aravind L. Spout. a class of methyltransferases that includes spoU and trmD rna methylase superfamilies and novel superfamilies of predicted prokaryotic rna methylases J. Mol. Microbiol. Biotechnol. 4:2002;71-75.
    • (2002) J. Mol. Microbiol. Biotechnol. , vol.4 , pp. 71-75
    • Anantharaman, V.1    Koonin, E.V.2    Aravind, L.3
  • 5
    • 0032953571 scopus 로고    scopus 로고
    • The yeast Saccharomyces cerevisiae YDL112w ORF encodes the putative 2′-O-ribose methyltransferase catalyzing the formation of Gm18 in tRNAs
    • Cavaillé J., Chetouani F., Bachellerie J.-P. The yeast Saccharomyces cerevisiae YDL112w ORF encodes the putative 2′-O-ribose methyltransferase catalyzing the formation of Gm18 in tRNAs. RNA. 5:1999;66-81.
    • (1999) RNA , vol.5 , pp. 66-81
    • Cavaillé, J.1    Chetouani, F.2    Bachellerie, J.-P.3
  • 6
    • 0035883736 scopus 로고    scopus 로고
    • AdoMet-dependent methylation, DNA methyltransferases and base flipping
    • Cheng X., Roberts R. AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res. 29:2001;3784-3795.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 3784-3795
    • Cheng, X.1    Roberts, R.2
  • 7
    • 0028103275 scopus 로고
    • The CCP4 (Collaborative Computational Project 4) suite: Programs for protein crystallography
    • CCP4 The CCP4 (Collaborative Computational Project 4) suite. programs for protein crystallography Acta Crystallogr. D. 50:1994;760-763.
    • (1994) Acta Crystallogr. D , vol.50 , pp. 760-763
  • 8
    • 0031058188 scopus 로고    scopus 로고
    • Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods
    • de La Fortelle E., Bricogne G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276:1997;472-494.
    • (1997) Methods Enzymol. , vol.276 , pp. 472-494
    • De La Fortelle, E.1    Bricogne, G.2
  • 9
    • 0031045585 scopus 로고    scopus 로고
    • Preparation of selenomethionyl proteins for phase determination
    • Doublié S. Preparation of selenomethionyl proteins for phase determination. Methods Enzymol. 276:1997;523-530.
    • (1997) Methods Enzymol. , vol.276 , pp. 523-530
    • Doublié, S.1
  • 11
    • 0035966271 scopus 로고    scopus 로고
    • Cocrystal structure of a tRNA Ψ55 pseudouridine synthetase: Nucleotide flipping by an RNA-modification enzyme
    • Hoang C., Ferre-D'Amare A. Cocrystal structure of a tRNA Ψ55 pseudouridine synthetase. nucleotide flipping by an RNA-modification enzyme Cell. 107:2001;929-939.
    • (2001) Cell , vol.107 , pp. 929-939
    • Hoang, C.1    Ferre-D'Amare, A.2
  • 13
    • 0036206498 scopus 로고    scopus 로고
    • Identification and characterization of tRNA(Gm18)methyltransferase from Thermus thermophilus HB8: Domain structure and conserved amino acid sequence motifs
    • Hori H., Suzuki T., Sugawara K., Inoue Y., Shibata T., Kuramitsu S., Yokoyama S., Oshima T., Watanabe K. Identification and characterization of tRNA(Gm18)methyltransferase from Thermus thermophilus HB8. domain structure and conserved amino acid sequence motifs Genes Cells. 7:2002;259-272.
    • (2002) Genes Cells , vol.7 , pp. 259-272
    • Hori, H.1    Suzuki, T.2    Sugawara, K.3    Inoue, Y.4    Shibata, T.5    Kuramitsu, S.6    Yokoyama, S.7    Oshima, T.8    Watanabe, K.9
  • 14
    • 0042591322 scopus 로고    scopus 로고
    • Aquifex aeolicus tRNA (Gm18) methyltransferase has unique substrate specificity. tRNA recognition mechanism of the enzyme
    • Hori H., Kubota S., Watanabe K., Kim J.M., Ogasawara T., Sawasaki T., Endo Y. Aquifex aeolicus tRNA (Gm18) methyltransferase has unique substrate specificity. tRNA recognition mechanism of the enzyme. J. Biol. Chem. 278:2003;25081-25090.
    • (2003) J. Biol. Chem. , vol.278 , pp. 25081-25090
    • Hori, H.1    Kubota, S.2    Watanabe, K.3    Kim, J.M.4    Ogasawara, T.5    Sawasaki, T.6    Endo, Y.7
  • 15
    • 0038613099 scopus 로고    scopus 로고
    • Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme
    • Ishitani R., Nureki O., Nameki N., Okada N., Nishimura S., Yokoyama S. Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell. 113:2003;383-394.
    • (2003) Cell , vol.113 , pp. 383-394
    • Ishitani, R.1    Nureki, O.2    Nameki, N.3    Okada, N.4    Nishimura, S.5    Yokoyama, S.6
  • 17
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones T.A., Zou J.-Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47:1991;110-119.
    • (1991) Acta Crystallogr. a , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.-Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 18
    • 0026524798 scopus 로고
    • Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2′-hydroxyl group
    • Kawai G., Yamamoto Y., Kamimura T., Sekine M., Hata T., Iimori T., Watanabe T., Miyazawa T., Yokoyama S. Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2′-hydroxyl group. Biochemistry. 31:1992;1040-1046.
    • (1992) Biochemistry , vol.31 , pp. 1040-1046
    • Kawai, G.1    Yamamoto, Y.2    Kamimura, T.3    Sekine, M.4    Hata, T.5    Iimori, T.6    Watanabe, T.7    Miyazawa, T.8    Yokoyama, S.9
  • 19
    • 0018832937 scopus 로고
    • Thermally induced biosynthesis of 2′-O-methylguanosine in tRNA from an extreme thermophile, Thermus thermophilus HB27
    • Kumagai I., Watanabe K., Oshima T. Thermally induced biosynthesis of 2′-O-methylguanosine in tRNA from an extreme thermophile, Thermus thermophilus HB27. Proc. Natl. Acad. Sci. USA. 77:1980;1922-1926.
    • (1980) Proc. Natl. Acad. Sci. USA , vol.77 , pp. 1922-1926
    • Kumagai, I.1    Watanabe, K.2    Oshima, T.3
  • 20
  • 21
    • 0141592367 scopus 로고    scopus 로고
    • 1G37)methyltransferase from Aquifex aeolicus at 2.6 Å resolution: A novel methyltransferase fold
    • 1G37)methyltransferase from Aquifex aeolicus at 2.6 Å resolution. a novel methyltransferase fold Proteins. 53:2003;326-328.
    • (2003) Proteins , vol.53 , pp. 326-328
    • Liu, J.1    Wang, W.2    Shin, D.H.3    Yokota, H.4    Kim, R.5    Kim, S.-H.6
  • 23
    • 0025267908 scopus 로고
    • Recognition sites of tRNA by a thermostable tRNA (guanosine-2′-)- methyltransferase from Thermus thermophilus HB27
    • Matsumoto T., Nishikawa K., Hori H., Ohta T., Miura K., Watanabe K. Recognition sites of tRNA by a thermostable tRNA (guanosine-2′-)- methyltransferase from Thermus thermophilus HB27. J. Biochem. (Tokyo). 107:1990;331-338.
    • (1990) J. Biochem. (Tokyo) , vol.107 , pp. 331-338
    • Matsumoto, T.1    Nishikawa, K.2    Hori, H.3    Ohta, T.4    Miura, K.5    Watanabe, K.6
  • 24
    • 0036774065 scopus 로고    scopus 로고
    • The structure of the RmlB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot
    • Michel G., Sauvé V., Larocque R., Li Y., Matte A., Cygler M. The structure of the RmlB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot. Structure. 10:2002;1303-1315.
    • (2002) Structure , vol.10 , pp. 1303-1315
    • Michel, G.1    Sauvé, V.2    Larocque, R.3    Li, Y.4    Matte, A.5    Cygler, M.6
  • 26
    • 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
  • 27
    • 1842404152 scopus 로고    scopus 로고
    • The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for (Gm18) 2′-O-methyltransferase activity
    • Persson B.C., Jager G., Gustaffson C. The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for (Gm18) 2′-O- methyltransferase activity. Nucleic Acids Res. 25:1997;3969-3973.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3969-3973
    • Persson, B.C.1    Jager, G.2    Gustaffson, C.3
  • 29
    • 0034710671 scopus 로고    scopus 로고
    • A deeply knotted protein structure and how it might fold
    • Taylor W.R. A deeply knotted protein structure and how it might fold. Nature. 406:2000;916-919.
    • (2000) Nature , vol.406 , pp. 916-919
    • Taylor, W.R.1
  • 30
    • 19944409045 scopus 로고    scopus 로고
    • The design and implementation of SnB version 2.0
    • Weeks C.M., Miller R. The design and implementation of SnB version 2.0. J. Appl. Crystallogr. 32:1999;120-124.
    • (1999) J. Appl. Crystallogr. , vol.32 , pp. 120-124
    • Weeks, C.M.1    Miller, R.2
  • 31
    • 0141596159 scopus 로고    scopus 로고
    • Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate
    • Xie W., Liu X., Huang R.H. Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate. Nat. Struct. Biol. 10:2003;781-788.
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 781-788
    • Xie, W.1    Liu, X.2    Huang, R.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.