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Volumn 17, Issue 3, 2007, Pages 293-301

Complexes of tRNA and maturation enzymes: shaping up for translation

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE DEAMINASE; INOSINE; TRANSFER RNA;

EID: 34347402424     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2007.05.002     Document Type: Review
Times cited : (24)

References (49)
  • 2
    • 19444369242 scopus 로고    scopus 로고
    • Enter transfer RNA
    • Hoagland M. Enter transfer RNA. Nature 431 (2004) 249
    • (2004) Nature , vol.431 , pp. 249
    • Hoagland, M.1
  • 4
    • 0024392753 scopus 로고
    • Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 Å resolution
    • Rould M.A., Perona J.J., Soll D., and Steitz T.A. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 Å resolution. Science 246 (1989) 1135-1142
    • (1989) Science , vol.246 , pp. 1135-1142
    • Rould, M.A.1    Perona, J.J.2    Soll, D.3    Steitz, T.A.4
  • 6
    • 33748582906 scopus 로고    scopus 로고
    • Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements
    • Phe) bound to the P and E sites is described at 3.7 Å. The anticodon region of the tRNA at the P site base pairs with codon nucleotides and interacts with 16S rRNA and S13 protein. The wobble base is observed to stack with 16S bases. Interestingly, tRNA in the P site is deformed slightly.
    • Phe) bound to the P and E sites is described at 3.7 Å. The anticodon region of the tRNA at the P site base pairs with codon nucleotides and interacts with 16S rRNA and S13 protein. The wobble base is observed to stack with 16S bases. Interestingly, tRNA in the P site is deformed slightly.
    • (2006) Cell , vol.126 , pp. 1065-1077
    • Korostelev, A.1    Trakhanov, S.2    Laurberg, M.3    Noller, H.F.4
  • 9
    • 24644437810 scopus 로고    scopus 로고
    • RNA structure: reading the ribosome
    • An excellent description of RNA structures by comparing features found in tRNA, in ribozymes and in rRNA.
    • Noller H.F. RNA structure: reading the ribosome. Science 309 (2005) 1508-1514. An excellent description of RNA structures by comparing features found in tRNA, in ribozymes and in rRNA.
    • (2005) Science , vol.309 , pp. 1508-1514
    • Noller, H.F.1
  • 11
    • 0031456444 scopus 로고    scopus 로고
    • Aminoacyl-tRNA synthetases
    • Cusack S. Aminoacyl-tRNA synthetases. Curr Opin Struct Biol 7 (1997) 881-889
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 881-889
    • Cusack, S.1
  • 12
    • 0037439213 scopus 로고    scopus 로고
    • tRNA transfers to the limelight
    • Hopper A.K., and Phizicky E.M. tRNA transfers to the limelight. Genes Dev 17 (2003) 162-180
    • (2003) Genes Dev , vol.17 , pp. 162-180
    • Hopper, A.K.1    Phizicky, E.M.2
  • 13
    • 23844456923 scopus 로고    scopus 로고
    • Have tRNA, will travel
    • Phizicky E.M. Have tRNA, will travel. Proc Natl Acad Sci USA 102 (2005) 11127-11128
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 11127-11128
    • Phizicky, E.M.1
  • 14
    • 33745166320 scopus 로고    scopus 로고
    • RNase P: interface of the RNA and protein worlds
    • Evans D., Marquez S.M., and Pace N.R. RNase P: interface of the RNA and protein worlds. Trends Biochem Sci 31 (2006) 333-341
    • (2006) Trends Biochem Sci , vol.31 , pp. 333-341
    • Evans, D.1    Marquez, S.M.2    Pace, N.R.3
  • 16
    • 0029906943 scopus 로고    scopus 로고
    • Conformational flexibility of tRNA: structural changes in yeast tRNA(Asp) upon binding to aspartyl-tRNA synthetase
    • Rees B., Cavarelli J., and Moras D. Conformational flexibility of tRNA: structural changes in yeast tRNA(Asp) upon binding to aspartyl-tRNA synthetase. Biochimie 78 (1996) 624-631
    • (1996) Biochimie , vol.78 , pp. 624-631
    • Rees, B.1    Cavarelli, J.2    Moras, D.3
  • 17
    • 0025744320 scopus 로고
    • Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase
    • Rould M.A., Perona J.J., and Steitz T.A. Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature 352 (1991) 213-218
    • (1991) Nature , vol.352 , pp. 213-218
    • Rould, M.A.1    Perona, J.J.2    Steitz, T.A.3
  • 18
    • 0030962189 scopus 로고    scopus 로고
    • Structural and functional considerations of the aminoacylation reaction
    • Arnez J.G., and Moras D. Structural and functional considerations of the aminoacylation reaction. Trends Biochem Sci 22 (1997) 211-216
    • (1997) Trends Biochem Sci , vol.22 , pp. 211-216
    • Arnez, J.G.1    Moras, D.2
  • 19
    • 26044435441 scopus 로고    scopus 로고
    • Recent progress of structural biology of tRNA processing and modification
    • This review summarizes earlier structural studies on tRNA processing and modification enzymes. The described enzyme structures include RNase PH, tRNase Z, CCA-adding enzymes, archaeosine tRNA guanine-transglycosidases, queuosine tRNA guanine transglycosidase, U55 pseudouridine synthase TruB and RNA methyltransferase TrmH.
    • Nakanishi K., and Nureki O. Recent progress of structural biology of tRNA processing and modification. Mol Cells 19 (2005) 157-166. This review summarizes earlier structural studies on tRNA processing and modification enzymes. The described enzyme structures include RNase PH, tRNase Z, CCA-adding enzymes, archaeosine tRNA guanine-transglycosidases, queuosine tRNA guanine transglycosidase, U55 pseudouridine synthase TruB and RNA methyltransferase TrmH.
    • (2005) Mol Cells , vol.19 , pp. 157-166
    • Nakanishi, K.1    Nureki, O.2
  • 20
    • 0030433926 scopus 로고    scopus 로고
    • The ternary complex of aminoacylated tRNA and EF-Tu-GTP. Recognition of a bond and a fold
    • Nissen P., Kjeldgaard M., Thirup S., Clark B.F., and Nyborg J. The ternary complex of aminoacylated tRNA and EF-Tu-GTP. Recognition of a bond and a fold. Biochimie 78 (1996) 921-933
    • (1996) Biochimie , vol.78 , pp. 921-933
    • Nissen, P.1    Kjeldgaard, M.2    Thirup, S.3    Clark, B.F.4    Nyborg, J.5
  • 21
    • 0344874260 scopus 로고    scopus 로고
    • Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications
    • Marck C., and Grosjean H. Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications. RNA 9 (2003) 1516-1531
    • (2003) RNA , vol.9 , pp. 1516-1531
    • Marck, C.1    Grosjean, H.2
  • 22
    • 33750972578 scopus 로고    scopus 로고
    • Pseudouridine synthases
    • Hamma T., and Ferre-D'Amare A.R. Pseudouridine synthases. Chem Biol 13 (2006) 1125-1135
    • (2006) Chem Biol , vol.13 , pp. 1125-1135
    • Hamma, T.1    Ferre-D'Amare, A.R.2
  • 23
    • 29044449835 scopus 로고    scopus 로고
    • The tRNase Z family of proteins: physiological functions, substrate specificity and structural properties
    • This is a comprehensive review on the tRNase Z family of proteins. It summarizes the known functional properties of tRNase Z from various organisms and outlines our current understanding of this family of enzymes in light of the recent structural results.
    • Vogel A., Schilling O., Spath B., and Marchfelder A. The tRNase Z family of proteins: physiological functions, substrate specificity and structural properties. Biol Chem 386 (2005) 1253-1264. This is a comprehensive review on the tRNase Z family of proteins. It summarizes the known functional properties of tRNase Z from various organisms and outlines our current understanding of this family of enzymes in light of the recent structural results.
    • (2005) Biol Chem , vol.386 , pp. 1253-1264
    • Vogel, A.1    Schilling, O.2    Spath, B.3    Marchfelder, A.4
  • 24
    • 0020710638 scopus 로고
    • Precise excision of intervening sequences from precursor tRNAs by a membrane-associated yeast endonuclease
    • Peebles C.L., Gegenheimer P., and Abelson J. Precise excision of intervening sequences from precursor tRNAs by a membrane-associated yeast endonuclease. Cell 32 (1983) 525-536
    • (1983) Cell , vol.32 , pp. 525-536
    • Peebles, C.L.1    Gegenheimer, P.2    Abelson, J.3
  • 25
    • 0030730820 scopus 로고    scopus 로고
    • The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases
    • Trotta C.R., Miao F., Arn E.A., Stevens S.W., Ho C.K., Rauhut R., and Abelson J.N. The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases. Cell 89 (1997) 849-858
    • (1997) Cell , vol.89 , pp. 849-858
    • Trotta, C.R.1    Miao, F.2    Arn, E.A.3    Stevens, S.W.4    Ho, C.K.5    Rauhut, R.6    Abelson, J.N.7
  • 26
    • 27144449031 scopus 로고    scopus 로고
    • Structural characterization of the catalytic subunit of a novel RNA splicing endonuclease
    • Calvin K., Hall M.D., Xu F., Xue S., and Li H. Structural characterization of the catalytic subunit of a novel RNA splicing endonuclease. J Mol Biol 353 (2005) 952-960
    • (2005) J Mol Biol , vol.353 , pp. 952-960
    • Calvin, K.1    Hall, M.D.2    Xu, F.3    Xue, S.4    Li, H.5
  • 27
    • 21144453167 scopus 로고    scopus 로고
    • Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunctionalization
    • Tocchini-Valentini G.D., Fruscoloni P., and Tocchini-Valentini G.P. Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunctionalization. Proc Natl Acad Sci USA 102 (2005) 8933-8938
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 8933-8938
    • Tocchini-Valentini, G.D.1    Fruscoloni, P.2    Tocchini-Valentini, G.P.3
  • 28
    • 0024291338 scopus 로고
    • Substrate recognition and splice site determination in yeast tRNA splicing
    • Reyes V.M., and Abelson J. Substrate recognition and splice site determination in yeast tRNA splicing. Cell 55 (1988) 719-730
    • (1988) Cell , vol.55 , pp. 719-730
    • Reyes, V.M.1    Abelson, J.2
  • 29
    • 33646538487 scopus 로고    scopus 로고
    • RNA recognition and cleavage by a splicing endonuclease
    • The RNA splicing endonuclease is responsible for the removal of introns found in nuclear tRNA and all archaeal RNAs. The crystal structure of a dimeric splicing endonuclease bound to a pseudosymmetric BHB RNA containing the two splice junctions is described. The complex structure reveals the principle of sequence-independent recognition of two three-nucleotide bulges by the splicing endonuclease and shows the detailed atomic arrangement of the active sites for the RNA phosphodiester bond cleavage reaction.
    • Xue S., Calvin K., and Li H. RNA recognition and cleavage by a splicing endonuclease. Science 312 (2006) 906-910. The RNA splicing endonuclease is responsible for the removal of introns found in nuclear tRNA and all archaeal RNAs. The crystal structure of a dimeric splicing endonuclease bound to a pseudosymmetric BHB RNA containing the two splice junctions is described. The complex structure reveals the principle of sequence-independent recognition of two three-nucleotide bulges by the splicing endonuclease and shows the detailed atomic arrangement of the active sites for the RNA phosphodiester bond cleavage reaction.
    • (2006) Science , vol.312 , pp. 906-910
    • Xue, S.1    Calvin, K.2    Li, H.3
  • 30
    • 0032831634 scopus 로고    scopus 로고
    • Relationship between internucleotide linkage geometry and the stability of RNA
    • Soukup G.A., and Breaker R.R. Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5 (1999) 1308-1325
    • (1999) RNA , vol.5 , pp. 1308-1325
    • Soukup, G.A.1    Breaker, R.R.2
  • 31
    • 33745022625 scopus 로고    scopus 로고
    • Structure of the ubiquitous 3′ processing enzyme RNase Z bound to transfer RNA
    • Thr is described. tRNase Z contains an RNA-binding domain tethered to a metallohydrolase-like catalytic domain. The dimeric arrangement of the enzyme facilitates cross-subunit stabilization of the acceptor stem and the CCA trinucleotides, which explains the allosteric properties of the enzyme. Significant RNA structural remodeling at the 3′ end is observed upon association of the enzyme.
    • Thr is described. tRNase Z contains an RNA-binding domain tethered to a metallohydrolase-like catalytic domain. The dimeric arrangement of the enzyme facilitates cross-subunit stabilization of the acceptor stem and the CCA trinucleotides, which explains the allosteric properties of the enzyme. Significant RNA structural remodeling at the 3′ end is observed upon association of the enzyme.
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 376-377
    • Li de la Sierra-Gallay, I.1    Mathy, N.2    Pellegrini, O.3    Condon, C.4
  • 32
    • 14144251951 scopus 로고    scopus 로고
    • Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z
    • de la Sierra-Gallay I.L., Pellegrini O., and Condon C. Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z. Nature 433 (2005) 657-661
    • (2005) Nature , vol.433 , pp. 657-661
    • de la Sierra-Gallay, I.L.1    Pellegrini, O.2    Condon, C.3
  • 34
    • 0037099742 scopus 로고    scopus 로고
    • TadA, an essential tRNA-specific adenosine deaminase from Escherichia coli
    • Wolf J., Gerber A.P., and Keller W. TadA, an essential tRNA-specific adenosine deaminase from Escherichia coli. EMBO J 21 (2002) 3841-3851
    • (2002) EMBO J , vol.21 , pp. 3841-3851
    • Wolf, J.1    Gerber, A.P.2    Keller, W.3
  • 36
    • 0033600832 scopus 로고    scopus 로고
    • Singly and bifurcated hydrogen-bonded base-pairs in tRNA anticodon hairpins and ribozymes
    • Auffinger P., and Westhof E. Singly and bifurcated hydrogen-bonded base-pairs in tRNA anticodon hairpins and ribozymes. J Mol Biol 292 (1999) 467-483
    • (1999) J Mol Biol , vol.292 , pp. 467-483
    • Auffinger, P.1    Westhof, E.2
  • 37
    • 33747871555 scopus 로고    scopus 로고
    • tRNA residues that have coevolved with their anticodon to ensure uniform and accurate codon recognition
    • Olejniczak M., and Uhlenbeck O.C. tRNA residues that have coevolved with their anticodon to ensure uniform and accurate codon recognition. Biochimie 88 (2006) 943-950
    • (2006) Biochimie , vol.88 , pp. 943-950
    • Olejniczak, M.1    Uhlenbeck, O.C.2
  • 38
    • 0033527628 scopus 로고    scopus 로고
    • An adenosine deaminase that generates inosine at the wobble position of tRNAs
    • Gerber A.P., and Keller W. An adenosine deaminase that generates inosine at the wobble position of tRNAs. Science 286 (1999) 1146-1149
    • (1999) Science , vol.286 , pp. 1146-1149
    • Gerber, A.P.1    Keller, W.2
  • 39
    • 33747125139 scopus 로고    scopus 로고
    • Snapshots of tRNA sulphuration via an adenylated intermediate
    • Glu in three functional states illustrate one principle of tRNA anticodon stem-loop recognition, similar to what is observed for TadA; anticodon nucleotide U34 is splayed outwards to reach the enzyme active site for modification. Active site rearrangement enables identification of catalytically important residues. Two possible catalytic mechanisms are proposed.
    • Glu in three functional states illustrate one principle of tRNA anticodon stem-loop recognition, similar to what is observed for TadA; anticodon nucleotide U34 is splayed outwards to reach the enzyme active site for modification. Active site rearrangement enables identification of catalytically important residues. Two possible catalytic mechanisms are proposed.
    • (2006) Nature , vol.442 , pp. 419-424
    • Numata, T.1    Ikeuchi, Y.2    Fukai, S.3    Suzuki, T.4    Nureki, O.5
  • 40
    • 32344447144 scopus 로고    scopus 로고
    • A story with a good ending: tRNA 3′-end maturation by CCA-adding enzymes
    • Xiong Y., and Steitz T.A. A story with a good ending: tRNA 3′-end maturation by CCA-adding enzymes. Curr Opin Struct Biol 16 (2006) 12-17
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 12-17
    • Xiong, Y.1    Steitz, T.A.2
  • 41
    • 3943089138 scopus 로고    scopus 로고
    • Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template
    • Phe at low resolution and in three distinct complexes with the acceptor stem at better than 3.4 Å resolution offer significant insights into how CCA is polymerized without a nucleic acid template. The remarkable series of images captured at each enzymatic step - after the addition of C74, after the addition of C75 and after the addition of A76 - showed how the enzyme can switch specificity from CTP to ATP and that the enzyme active site is progressively altered by the elongating 3′ end of the tRNA. However, the lack of the TΨC loop in the model acceptor stem, which contacts the RNA-binding tail domain, could affect the precise ways in which the RNA and the active site residues rearrange in these crystals.
    • Phe at low resolution and in three distinct complexes with the acceptor stem at better than 3.4 Å resolution offer significant insights into how CCA is polymerized without a nucleic acid template. The remarkable series of images captured at each enzymatic step - after the addition of C74, after the addition of C75 and after the addition of A76 - showed how the enzyme can switch specificity from CTP to ATP and that the enzyme active site is progressively altered by the elongating 3′ end of the tRNA. However, the lack of the TΨC loop in the model acceptor stem, which contacts the RNA-binding tail domain, could affect the precise ways in which the RNA and the active site residues rearrange in these crystals.
    • (2004) Nature , vol.430 , pp. 640-645
    • Xiong, Y.1    Steitz, T.A.2
  • 42
    • 33750430666 scopus 로고    scopus 로고
    • Complete crystallographic analysis of the dynamics of CCA sequence addition
    • ••] in that the primer nucleotides splay out of the way so that the incoming NTP can be accommodated in the catalytic cleft. The sidechain of an important arginine residue was observed in different conformations depending on the polymerization stage; this is believed to achieve CTP/ATP discrimination.
    • ••] in that the primer nucleotides splay out of the way so that the incoming NTP can be accommodated in the catalytic cleft. The sidechain of an important arginine residue was observed in different conformations depending on the polymerization stage; this is believed to achieve CTP/ATP discrimination.
    • (2006) Nature , vol.443 , pp. 956-960
    • Tomita, K.1    Ishitani, R.2    Fukai, S.3    Nureki, O.4
  • 43
    • 33745587780 scopus 로고    scopus 로고
    • Structural basis of RNA-dependent recruitment of glutamine to the genetic code
    • Gln-specific bases of the acceptor stem are recognized by the enzyme. The structure also sheds light on the mechanism of ammonia recruitment through an ∼40 Å tunnel and repeating hydrogen bonding.
    • Gln-specific bases of the acceptor stem are recognized by the enzyme. The structure also sheds light on the mechanism of ammonia recruitment through an ∼40 Å tunnel and repeating hydrogen bonding.
    • (2006) Science , vol.312 , pp. 1950-1954
    • Oshikane, H.1    Sheppard, K.2    Fukai, S.3    Nakamura, Y.4    Ishitani, R.5    Numata, T.6    Sherrer, R.L.7    Feng, L.8    Schmitt, E.9    Panvert, M.10
  • 44
    • 0141596159 scopus 로고    scopus 로고
    • Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate
    • Xie W., Liu X., and 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
  • 45
    • 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., and 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
  • 47
    • 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
  • 48
    • 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
  • 49
    • 2042479408 scopus 로고    scopus 로고
    • Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3′ end formation
    • Paushkin S.V., Patel M., Furia B.S., Peltz S.W., and Trotta C.R. Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3′ end formation. Cell 117 (2004) 311-321
    • (2004) Cell , vol.117 , pp. 311-321
    • Paushkin, S.V.1    Patel, M.2    Furia, B.S.3    Peltz, S.W.4    Trotta, C.R.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.