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Volumn 367, Issue 5, 2007, Pages 1459-1470

The Crystal Structure of E. coli rRNA Pseudouridine Synthase RluE

Author keywords

protein RNA complex; ribosome; RNA modifying enzyme; substrate specificity; X ray crystallography

Indexed keywords

ARGININE; ASPARTIC ACID; ESCHERICHIA COLI PROTEIN; PEPTIDYLTRANSFERASE; PROTEIN RLUE; PSEUDOURIDINE; RIBOSOME RNA; RNA 23S; SYNTHETASE; TYROSINE; UNCLASSIFIED DRUG;

EID: 33947176022     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.01.084     Document Type: Article
Times cited : (10)

References (50)
  • 2
    • 0037029086 scopus 로고    scopus 로고
    • Ribosomal RNA pseudouridines and pseudouridine synthases
    • Ofengand J. Ribosomal RNA pseudouridines and pseudouridine synthases. FEBS Letters 514 (2002) 17-25
    • (2002) FEBS Letters , vol.514 , pp. 17-25
    • Ofengand, J.1
  • 3
    • 0027453260 scopus 로고
    • Multiple pseudouridine synthase activities for small nuclear RNAs
    • Patton J.R. Multiple pseudouridine synthase activities for small nuclear RNAs. Biochem. J. 290 (1993) 595-600
    • (1993) Biochem. J. , vol.290 , pp. 595-600
    • Patton, J.R.1
  • 4
    • 0025370090 scopus 로고
    • Transfer RNA pseudouridine synthases in Saccharomyces cerevisiae
    • Samuelsson T., and Olsson M. Transfer RNA pseudouridine synthases in Saccharomyces cerevisiae. J. Biol. Chem. 265 (1990) 8782-8787
    • (1990) J. Biol. Chem. , vol.265 , pp. 8782-8787
    • Samuelsson, T.1    Olsson, M.2
  • 5
    • 0033534387 scopus 로고    scopus 로고
    • Stabilization of the anticodon stem-loop of tRNALys,3 by an A+-C base-pair and by pseudouridine
    • Durant P.C., and Davis D.R. Stabilization of the anticodon stem-loop of tRNALys,3 by an A+-C base-pair and by pseudouridine. J. Mol. Biol. 285 (1999) 115-131
    • (1999) J. Mol. Biol. , vol.285 , pp. 115-131
    • Durant, P.C.1    Davis, D.R.2
  • 6
    • 0033199501 scopus 로고    scopus 로고
    • Structural and functional roles of the N1- and N3-protons of psi at tRNA's position 39
    • Yarian C.S., Basti M.M., Cain R.J., Ansari G., Guenther R.H., Sochacka E., et al. Structural and functional roles of the N1- and N3-protons of psi at tRNA's position 39. Nucl. Acids Res. 27 (1999) 3543-43549
    • (1999) Nucl. Acids Res. , vol.27 , pp. 3543-43549
    • Yarian, C.S.1    Basti, M.M.2    Cain, R.J.3    Ansari, G.4    Guenther, R.H.5    Sochacka, E.6
  • 7
    • 0033582628 scopus 로고    scopus 로고
    • A computational screen for methylation guide snoRNAs in yeast
    • Lowe T.M., and Eddy S.R. A computational screen for methylation guide snoRNAs in yeast. Science 283 (1999) 1168-1171
    • (1999) Science , vol.283 , pp. 1168-1171
    • Lowe, T.M.1    Eddy, S.R.2
  • 8
    • 0032894591 scopus 로고    scopus 로고
    • A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae
    • Samarsky D.A., and Fournier M.J. A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae. Nucl. Acids Res. 27 (1999) 161-164
    • (1999) Nucl. Acids Res. , vol.27 , pp. 161-164
    • Samarsky, D.A.1    Fournier, M.J.2
  • 9
    • 0032718276 scopus 로고    scopus 로고
    • Point mutations in yeast CBF5 can abolish in vivo pseudouridylation of rRNA
    • Zebarjadian Y., King T., Fournier M.J., Clarke L., and Carbon J. Point mutations in yeast CBF5 can abolish in vivo pseudouridylation of rRNA. Mol. Cell Biol. 19 (1999) 7461-7472
    • (1999) Mol. Cell Biol. , vol.19 , pp. 7461-7472
    • Zebarjadian, Y.1    King, T.2    Fournier, M.J.3    Clarke, L.4    Carbon, J.5
  • 10
    • 0029258983 scopus 로고
    • Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli
    • Nurse K., Wrzesinski J., Bakin A., Lane B.G., and Ofengand J. Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli. RNA 1 (1995) 102-112
    • (1995) RNA , vol.1 , pp. 102-112
    • Nurse, K.1    Wrzesinski, J.2    Bakin, A.3    Lane, B.G.4    Ofengand, J.5
  • 11
    • 0032488657 scopus 로고    scopus 로고
    • A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophilic catalyst
    • Huang L., Pookanjanatavip M., Gu X., and Santi D.V. A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophilic catalyst. Biochemistry 37 (1998) 344-351
    • (1998) Biochemistry , vol.37 , pp. 344-351
    • Huang, L.1    Pookanjanatavip, M.2    Gu, X.3    Santi, D.V.4
  • 12
    • 0029313081 scopus 로고
    • A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi 746 in 23S RNA is also specific for psi 32 in tRNA(phe)
    • Wrzesinski J., Nurse K., Bakin A., Lane B.G., and Ofengand J. A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi 746 in 23S RNA is also specific for psi 32 in tRNA(phe). RNA 1 (1995) 437-448
    • (1995) RNA , vol.1 , pp. 437-448
    • Wrzesinski, J.1    Nurse, K.2    Bakin, A.3    Lane, B.G.4    Ofengand, J.5
  • 13
    • 0029832294 scopus 로고    scopus 로고
    • Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes
    • Gustafsson C., Reid R., Greene P.J., and Santi D.V. Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes. Nucl. Acids Res. 24 (1996) 3756-3762
    • (1996) Nucl. Acids Res. , vol.24 , pp. 3756-3762
    • Gustafsson, C.1    Reid, R.2    Greene, P.J.3    Santi, D.V.4
  • 14
    • 0038475918 scopus 로고    scopus 로고
    • A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya
    • Kaya Y., and Ofengand J. A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. RNA 9 (2003) 711-721
    • (2003) RNA , vol.9 , pp. 711-721
    • Kaya, Y.1    Ofengand, J.2
  • 15
    • 0029945504 scopus 로고    scopus 로고
    • Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases
    • Koonin E.V. Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases. Nucl. Acids Res. 24 (1996) 2411-2415
    • (1996) Nucl. Acids Res. , vol.24 , pp. 2411-2415
    • Koonin, E.V.1
  • 16
    • 2442450595 scopus 로고    scopus 로고
    • Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold
    • Kaya Y., Del Campo M., Ofengand J., and Malhotra A. Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold. J. Biol. Chem. 279 (2004) 18107-18110
    • (2004) J. Biol. Chem. , vol.279 , pp. 18107-18110
    • Kaya, Y.1    Del Campo, M.2    Ofengand, J.3    Malhotra, A.4
  • 17
    • 2642517964 scopus 로고    scopus 로고
    • Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft
    • Chaudhuri B.N., Chan S., Perry L.J., and Yeates T.O. Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft. J. Biol. Chem. 279 (2004) 24585-24591
    • (2004) J. Biol. Chem. , vol.279 , pp. 24585-24591
    • Chaudhuri, B.N.1    Chan, S.2    Perry, L.J.3    Yeates, T.O.4
  • 18
    • 1642580818 scopus 로고    scopus 로고
    • Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli
    • Del Campo M., Ofengand J., and Malhotra A. Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli. RNA 10 (2004) 231-239
    • (2004) RNA , vol.10 , pp. 231-239
    • Del Campo, M.1    Ofengand, J.2    Malhotra, A.3
  • 19
    • 2342610542 scopus 로고    scopus 로고
    • X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold
    • Ericsson U.B., Nordlund P., and Hallberg B.M. X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. FEBS Letters 565 (2004) 59-64
    • (2004) FEBS Letters , vol.565 , pp. 59-64
    • Ericsson, U.B.1    Nordlund, P.2    Hallberg, B.M.3
  • 20
    • 0033987499 scopus 로고    scopus 로고
    • The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I
    • Foster P.G., Huang L., Santi D.V., and Stroud R.M. The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I. Nature Struct. Biol. 7 (2000) 23-27
    • (2000) Nature Struct. Biol. , vol.7 , pp. 23-27
    • Foster, P.G.1    Huang, L.2    Santi, D.V.3    Stroud, R.M.4
  • 21
    • 33751013845 scopus 로고    scopus 로고
    • Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure
    • Hoang C., Chen J., Vizthum C.A., Kandel J.M., Hamilton C.S., Mueller E.G., and Ferre-D'Amare A.R. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol. Cell 24 (2006) 535-545
    • (2006) Mol. Cell , vol.24 , pp. 535-545
    • Hoang, C.1    Chen, J.2    Vizthum, C.A.3    Kandel, J.M.4    Hamilton, C.S.5    Mueller, E.G.6    Ferre-D'Amare, A.R.7
  • 22
    • 0035966271 scopus 로고    scopus 로고
    • Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme
    • Hoang C., and Ferre-D'Amare A.R. Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme. Cell 107 (2001) 929-939
    • (2001) Cell , vol.107 , pp. 929-939
    • Hoang, C.1    Ferre-D'Amare, A.R.2
  • 23
    • 3042618760 scopus 로고    scopus 로고
    • Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold
    • Hoang C., and Ferre-D'Amare A.R. Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold. Rna 10 (2004) 1026-1033
    • (2004) Rna , vol.10 , pp. 1026-1033
    • Hoang, C.1    Ferre-D'Amare, A.R.2
  • 25
    • 9744240603 scopus 로고    scopus 로고
    • Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli
    • Mizutani K., Machida Y., Unzai S., Park S.Y., and Tame J.R. Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli. Biochemistry 43 (2004) 4454-4463
    • (2004) Biochemistry , vol.43 , pp. 4454-4463
    • Mizutani, K.1    Machida, Y.2    Unzai, S.3    Park, S.Y.4    Tame, J.R.5
  • 26
    • 0242331664 scopus 로고    scopus 로고
    • Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit
    • Pan H., Agarwalla S., Moustakas D.T., Finer-Moore J., and Stroud R.M. Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit. Proc. Natl Acad. Sci. USA 100 (2003) 12648-12653
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 12648-12653
    • Pan, H.1    Agarwalla, S.2    Moustakas, D.T.3    Finer-Moore, J.4    Stroud, R.M.5
  • 27
    • 2542578632 scopus 로고    scopus 로고
    • Conformational change of pseudouridine 55 synthase upon its association with RNA substrate
    • Phannachet K., and Huang R.H. Conformational change of pseudouridine 55 synthase upon its association with RNA substrate. Nucl. Acids Res. 32 (2004) 1422-1429
    • (2004) Nucl. Acids Res. , vol.32 , pp. 1422-1429
    • Phannachet, K.1    Huang, R.H.2
  • 28
    • 0344687349 scopus 로고    scopus 로고
    • Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli
    • Sivaraman J., Iannuzzi P., Cygler M., and Matte A. Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli. J. Mol. Biol. 335 (2004) 87-101
    • (2004) J. Mol. Biol. , vol.335 , pp. 87-101
    • Sivaraman, J.1    Iannuzzi, P.2    Cygler, M.3    Matte, A.4
  • 30
    • 33744920298 scopus 로고    scopus 로고
    • Domain organization and crystal structure of the catalytic domain of E. coli RluF, a pseudouridine synthase that acts on 23S rRNA
    • Sunita S., Zhenxing H., Swaathi J., Cygler M., Matte A., and Sivaraman J. Domain organization and crystal structure of the catalytic domain of E. coli RluF, a pseudouridine synthase that acts on 23S rRNA. J. Mol. Biol. 359 (2006) 998-1009
    • (2006) J. Mol. Biol. , vol.359 , pp. 998-1009
    • Sunita, S.1    Zhenxing, H.2    Swaathi, J.3    Cygler, M.4    Matte, A.5    Sivaraman, J.6
  • 31
    • 0035163770 scopus 로고    scopus 로고
    • Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli
    • Del Campo M., Kaya Y., and Ofengand J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603-1615
    • (2001) RNA , vol.7 , pp. 1603-1615
    • Del Campo, M.1    Kaya, Y.2    Ofengand, J.3
  • 32
    • 0031813839 scopus 로고    scopus 로고
    • A 20-kilodalton N-terminal fragment of the D15 protein contains a protective epitope(s) against Haemophilus influenzae type a and type b
    • Yang Y., Thomas W.R., Chong P., Loosmore S.M., and Klein M.H. A 20-kilodalton N-terminal fragment of the D15 protein contains a protective epitope(s) against Haemophilus influenzae type a and type b. Infect. Immun. 66 (1998) 3349-3354
    • (1998) Infect. Immun. , vol.66 , pp. 3349-3354
    • Yang, Y.1    Thomas, W.R.2    Chong, P.3    Loosmore, S.M.4    Klein, M.H.5
  • 33
    • 14844293080 scopus 로고    scopus 로고
    • A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function
    • Lee T.T., Agarwalla S., and Stroud R.M. A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell 120 (2005) 599-611
    • (2005) Cell , vol.120 , pp. 599-611
    • Lee, T.T.1    Agarwalla, S.2    Stroud, R.M.3
  • 34
    • 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: Struct. Funct. Genet. 40 (2000) 502-511
    • (2000) Proteins: Struct. Funct. Genet. , vol.40 , pp. 502-511
    • Cuff, J.A.1    Barton, G.J.2
  • 35
    • 84860507958 scopus 로고    scopus 로고
    • Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms
    • Cheng J., and Baldi P. Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics 21 (2005) i75-i84
    • (2005) Bioinformatics , vol.21
    • Cheng, J.1    Baldi, P.2
  • 37
    • 0029884694 scopus 로고    scopus 로고
    • GOR method for predicting protein secondary structure from amino acid sequence
    • Garnier J., Gibrat J.F., and Robson B. GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol. 266 (1996) 540-553
    • (1996) Methods Enzymol. , vol.266 , pp. 540-553
    • Garnier, J.1    Gibrat, J.F.2    Robson, B.3
  • 38
    • 28244473650 scopus 로고    scopus 로고
    • Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase
    • Phannachet K., Elias Y., and Huang R.H. Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase. Biochemistry 44 (2005) 15488-15494
    • (2005) Biochemistry , vol.44 , pp. 15488-15494
    • Phannachet, K.1    Elias, Y.2    Huang, R.H.3
  • 40
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar I., Atilgan A.R., and Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2 (1997) 173-181
    • (1997) Fold. Des. , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 41
    • 0031059866 scopus 로고    scopus 로고
    • Processing of x-ray diffraction data collected in oscillation mode
    • Otwinowski Z., and 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
  • 44
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D 53 (1997) 240-255
    • (1997) Acta Crystallog. sect. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 45
  • 47
    • 0026319199 scopus 로고
    • Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls A., Sharp K.A., and 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
  • 49
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-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
  • 50
    • 0032961270 scopus 로고    scopus 로고
    • ESPript: analysis of multiple sequence alignments in PostScript
    • Gouet P., Courcelle E., Stuart D.I., and Metoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15 (1999) 305-308
    • (1999) Bioinformatics , vol.15 , pp. 305-308
    • Gouet, P.1    Courcelle, E.2    Stuart, D.I.3    Metoz, F.4


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