메뉴 건너뛰기




Volumn 40, Issue 16, 2012, Pages 8144-8154

How an exonuclease decides where to stop in trimming of nucleic acids: Crystal structures of RNase T-product complexes

Author keywords

[No Author keywords available]

Indexed keywords

DEDDH EXONUCLEASE; DINUCLEOTIDE; DOUBLE STRANDED DNA; EXONUCLEASE; NUCLEIC ACID; RIBONUCLEASE; RIBONUCLEASE T; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

EID: 84870546369     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks548     Document Type: Article
Times cited : (34)

References (49)
  • 2
    • 0035283033 scopus 로고    scopus 로고
    • Exoribonuclease superfamilies: Structural analysis and phylogenetic distribution
    • Zuo, Y. and Deutscher, M.P. (2001) Exoribonuclease superfamilies: structural analysis and phylogenetic distribution. Nucleic Acids Res., 29, 1017-1026.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 1017-1026
    • Zuo, Y.1    Deutscher, M.P.2
  • 7
    • 77958114725 scopus 로고    scopus 로고
    • The cytosolic exonuclease TREX1 inhibits the innate immune response to human immunodeficiency virus type 1
    • Yan, N., Regalado-Magdos, A.D., Stiggelbout, B., Lee-Kirsch, M.A. and Lieberman, J. (2010) The cytosolic exonuclease TREX1 inhibits the innate immune response to human immunodeficiency virus type 1. Nat. Immunol., 11, 1005-1013.
    • (2010) Nat. Immunol. , vol.11 , pp. 1005-1013
    • Yan, N.1    Regalado-Magdos, A.D.2    Stiggelbout, B.3    Lee-Kirsch, M.A.4    Lieberman, J.5
  • 8
    • 77958147729 scopus 로고    scopus 로고
    • Host DNase TREX1 hides HIV from DNA sensors
    • Geijtenbeek, T.B. (2010) Host DNase TREX1 hides HIV from DNA sensors. Nat. Immunol., 11, 979-980.
    • (2010) Nat. Immunol. , vol.11 , pp. 979-980
    • Geijtenbeek, T.B.1
  • 9
    • 79952303123 scopus 로고    scopus 로고
    • Structure of the Lassa virus nucleoprotein reveals a dsRNA-specific 30 to 50 exonuclease activity essential for immune suppression
    • Hastie, K.M., Kimberlin, C.R., Zandonatti, M.A., MacRae, I.J. and Saphire, E.O. (2011) Structure of the Lassa virus nucleoprotein reveals a dsRNA-specific 30 to 50 exonuclease activity essential for immune suppression. Proc. Natl Acad. Sci. USA, 108, 2396-2401.
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 2396-2401
    • Hastie, K.M.1    Kimberlin, C.R.2    Zandonatti, M.A.3    MacRae, I.J.4    Saphire, E.O.5
  • 10
    • 58249107985 scopus 로고    scopus 로고
    • Crystal structure of CRN-4: Implications for domain function in apoptotic DNA degradation
    • Hsiao, Y.Y., Nakagawa, A., Shi, Z., Mitani, S., Xue, D. and Yuan, H.S. (2009) Crystal structure of CRN-4: implications for domain function in apoptotic DNA degradation. Mol. Cell. Biol., 29, 448-457.
    • (2009) Mol. Cell. Biol. , vol.29 , pp. 448-457
    • Hsiao, Y.Y.1    Nakagawa, A.2    Shi, Z.3    Mitani, S.4    Xue, D.5    Yuan, H.S.6
  • 11
    • 33845264383 scopus 로고    scopus 로고
    • Genetic and biochemical characterization of Drosophila Snipper: A promiscuous member of the metazoan 30hExo/ERI-1 family of 30 to 50 exonucleases
    • Kupsco, J.M., Wu, M.J., Marzluff, W.F., Thapar, R. and Duronio, R.J. (2006) Genetic and biochemical characterization of Drosophila Snipper: A promiscuous member of the metazoan 30hExo/ERI-1 family of 30 to 50 exonucleases. RNA, 12, 2103-2117.
    • (2006) RNA , vol.12 , pp. 2103-2117
    • Kupsco, J.M.1    Wu, M.J.2    Marzluff, W.F.3    Thapar, R.4    Duronio, R.J.5
  • 12
    • 33750044572 scopus 로고    scopus 로고
    • Characterization of 30hExo a 30 exonuclease specifically interacting with the 30 end of histone mRNA
    • Yang, X.C., Purdy, M., Marzluff, W.F. and Dominski, Z. (2006) Characterization of 30hExo, a 30 exonuclease specifically interacting with the 30 end of histone mRNA. J. Biol. Chem., 281, 30447-30454.
    • (2006) J. Biol. Chem. , vol.281 , pp. 30447-30454
    • Yang, X.C.1    Purdy, M.2    Marzluff, W.F.3    Dominski, Z.4
  • 13
    • 0141888419 scopus 로고    scopus 로고
    • A 30 exonuclease that specifically interacts with the 30 end of histone mRNA
    • Dominski, Z., Yang, X.C., Kaygun, H., Dadlez, M. and Marzluff, W.F. (2003) A 30 exonuclease that specifically interacts with the 30 end of histone mRNA. Mol. Cell, 12, 295-305.
    • (2003) Mol. Cell , vol.12 , pp. 295-305
    • Dominski, Z.1    Yang, X.C.2    Kaygun, H.3    Dadlez, M.4    Marzluff, W.F.5
  • 14
    • 1342346710 scopus 로고    scopus 로고
    • A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans
    • Kennedy, S., Wang, D. and Ruvkun, G. (2004) A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature, 427, 645-649.
    • (2004) Nature , vol.427 , pp. 645-649
    • Kennedy, S.1    Wang, D.2    Ruvkun, G.3
  • 15
    • 80055089237 scopus 로고    scopus 로고
    • Mechanism of Exonuclease i stimulation by the single-stranded DNA-binding protein
    • Lu, D., Myers, A.R., George, N.P. and Keck, J.L. (2011) Mechanism of Exonuclease I stimulation by the single-stranded DNA-binding protein. Nucleic Acids Res., 39, 6536-6545.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 6536-6545
    • Lu, D.1    Myers, A.R.2    George, N.P.3    Keck, J.L.4
  • 16
    • 0033664281 scopus 로고    scopus 로고
    • Structure of Escherichia coli exonuclease i suggests how processivity is achieved
    • Breyer, W.A. and Matthews, B.W. (2000) Structure of Escherichia coli exonuclease I suggests how processivity is achieved. Nat. Struct. Biol., 7, 1125-1128.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 1125-1128
    • Breyer, W.A.1    Matthews, B.W.2
  • 17
    • 0035912937 scopus 로고    scopus 로고
    • The human interferon-and estrogen-regulated ISG20/HEM45 gene product degrades single-stranded RNA and DNA in vitro
    • Nguyen, L.H., Espert, L., Mechti, N. and Wilson, D.M. 3rd (2001) The human interferon-and estrogen-regulated ISG20/HEM45 gene product degrades single-stranded RNA and DNA in vitro. Biochemistry, 40, 7174-7179.
    • (2001) Biochemistry , vol.40 , pp. 7174-7179
    • Nguyen, L.H.1    Espert, L.2    Mechti, N.3    Wilson III, D.M.4
  • 18
    • 7544228191 scopus 로고    scopus 로고
    • Crystal structure of human ISG20, an interferoninduced antiviral ribonuclease
    • Horio, T., Murai, M., Inoue, T., Hamasaki, T., Tanaka, T. and Ohgi, T. (2004) Crystal structure of human ISG20, an interferoninduced antiviral ribonuclease. FEBS Lett., 577, 111-116.
    • (2004) FEBS Lett. , vol.577 , pp. 111-116
    • Horio, T.1    Murai, M.2    Inoue, T.3    Hamasaki, T.4    Tanaka, T.5    Ohgi, T.6
  • 19
    • 0033551137 scopus 로고    scopus 로고
    • Oligoribonuclease is an essential component of the mRNA decay pathway
    • Ghosh, S. and Deutscher, M.P. (1999) Oligoribonuclease is an essential component of the mRNA decay pathway. Proc. Natl Acad. Sci. USA, 96, 4372-4377.
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 4372-4377
    • Ghosh, S.1    Deutscher, M.P.2
  • 20
    • 28644436520 scopus 로고    scopus 로고
    • Structural insight into poly(A) binding and catalytic mechanism of human PARN
    • Wu, M., Reuter, M., Lilie, H., Liu, Y., Wahle, E. and Song, H. (2005) Structural insight into poly(A) binding and catalytic mechanism of human PARN. EMBO J., 24, 4082-4093.
    • (2005) EMBO J. , vol.24 , pp. 4082-4093
    • Wu, M.1    Reuter, M.2    Lilie, H.3    Liu, Y.4    Wahle, E.5    Song, H.6
  • 21
    • 0345832225 scopus 로고    scopus 로고
    • X-ray structure and activity of the yeast Pop2 protein: A nuclease subunit of the mRNA deadenylase complex
    • Thore, S., Mauxion, F., Seraphin, B. and Suck, D. (2003) X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex. EMBO Rep., 4, 1150-1155.
    • (2003) EMBO Rep. , vol.4 , pp. 1150-1155
    • Thore, S.1    Mauxion, F.2    Seraphin, B.3    Suck, D.4
  • 22
    • 0037119408 scopus 로고    scopus 로고
    • The physiological role of RNase T can be explained by its unusual substrate specificity
    • Zuo, Y. and Deutscher, M.P. (2002) The physiological role of RNase T can be explained by its unusual substrate specificity. J. Biol. Chem., 277, 29654-29661.
    • (2002) J. Biol. Chem. , vol.277 , pp. 29654-29661
    • Zuo, Y.1    Deutscher, M.P.2
  • 23
    • 0033569848 scopus 로고    scopus 로고
    • The DNase activity of RNase T and its application to DNA cloning
    • Zuo, Y. and Deutscher, M.P. (1999) The DNase activity of RNase T and its application to DNA cloning. Nucleic Acids Res., 27, 4077-4082.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4077-4082
    • Zuo, Y.1    Deutscher, M.P.2
  • 24
    • 0032951885 scopus 로고    scopus 로고
    • Maturation of 23S ribosomal RNA requires the exoribonuclease RNase T
    • Li, Z., Pandit, S. and Deutscher, M.P. (1999) Maturation of 23S ribosomal RNA requires the exoribonuclease RNase T. RNA, 5, 139-146.
    • (1999) RNA , vol.5 , pp. 139-146
    • Li, Z.1    Pandit, S.2    Deutscher, M.P.3
  • 25
    • 0029151159 scopus 로고
    • The tRNA processing enzyme RNase T is essential for maturation of 5S RNA
    • Li, Z. and Deutscher, M.P. (1995) The tRNA processing enzyme RNase T is essential for maturation of 5S RNA. Proc. Natl Acad. Sci. USA, 92, 6883-6886.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 6883-6886
    • Li, Z.1    Deutscher, M.P.2
  • 26
    • 0030576503 scopus 로고    scopus 로고
    • Maturation pathways for E. coli tRNA precursors: A random multienzyme process in vivo
    • Li, Z. and Deutscher, M.P. (1996) Maturation pathways for E. coli tRNA precursors: a random multienzyme process in vivo. Cell, 86, 503-512.
    • (1996) Cell , vol.86 , pp. 503-512
    • Li, Z.1    Deutscher, M.P.2
  • 27
    • 0037147310 scopus 로고    scopus 로고
    • Mechanism of action of RNase T. II. A structural and functional model of the enzyme
    • Zuo, Y. and Deutscher, M.P. (2002) Mechanism of action of RNase T. II. A structural and functional model of the enzyme. J. Biol. Chem., 277, 50160-50164.
    • (2002) J. Biol. Chem. , vol.277 , pp. 50160-50164
    • Zuo, Y.1    Deutscher, M.P.2
  • 28
    • 79952953767 scopus 로고    scopus 로고
    • Structural basis for RNA trimming by RNase T in stable RNA 30-end maturation
    • Hsiao, Y.Y., Yang, C.C., Lin, C.L., Lin, J.L., Duh, Y. and Yuan, H.S. (2011) Structural basis for RNA trimming by RNase T in stable RNA 30-end maturation. Nat. Chem. Biol., 7, 236-243.
    • (2011) Nat. Chem. Biol. , vol.7 , pp. 236-243
    • Hsiao, Y.Y.1    Yang, C.C.2    Lin, C.L.3    Lin, J.L.4    Duh, Y.5    Yuan, H.S.6
  • 29
    • 0031059866 scopus 로고    scopus 로고
    • "Processing of X-ray diffraction data collected in oscillation mode" methods in enzymology
    • Otwinowski, Z. and Minor, W. (1997) ''Processing of X-ray diffraction data collected in oscillation mode'', methods in enzymology. Macromol. Crystallogr. Part A, 276, 307-326.
    • (1997) Macromol. Crystallogr. Part A , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 30
    • 0037779018 scopus 로고    scopus 로고
    • A graphical user interface to the CCP4 program suite
    • Potterton, E., Briggs, P., Turkenburg, M. and Dodson, E. (2003) A graphical user interface to the CCP4 program suite. Acta. Cryst. D, 59, 1131-1137.
    • (2003) Acta. Cryst. D , vol.59 , pp. 1131-1137
    • Potterton, E.1    Briggs, P.2    Turkenburg, M.3    Dodson, E.4
  • 31
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building tools for molecular graphics
    • Emsley, P. and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta. Cryst. D, 60, 2126-2132.
    • (2004) Acta. Cryst. D , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 33
    • 56749157701 scopus 로고    scopus 로고
    • Structural and biochemical studies of TREX1 inhibition by metals. Identification of a new active histidine conserved in DEDDh exonucleases
    • Brucet, M., Querol-Audi, J., Bertlik, K., Lloberas, J., Fita, I. and Celada, A. (2008) Structural and biochemical studies of TREX1 inhibition by metals. Identification of a new active histidine conserved in DEDDh exonucleases. Protein Sci., 17, 2059-2069.
    • (2008) Protein Sci. , vol.17 , pp. 2059-2069
    • Brucet, M.1    Querol-Audi, J.2    Bertlik, K.3    Lloberas, J.4    Fita, I.5    Celada, A.6
  • 34
    • 0036229246 scopus 로고    scopus 로고
    • Structural basis for proofreading during replication of the Escherichia coli chromosome
    • Hamdan, S., Carr, P.D., Brown, S.E., Ollis, D.L. and Dixon, N.E. (2002) Structural basis for proofreading during replication of the Escherichia coli chromosome. Structure, 10, 535-546.
    • (2002) Structure , vol.10 , pp. 535-546
    • Hamdan, S.1    Carr, P.D.2    Brown, S.E.3    Ollis, D.L.4    Dixon, N.E.5
  • 35
    • 41549107524 scopus 로고    scopus 로고
    • RNA recognition by 30-to-5' exonucleases: The substrate perspective
    • Ibrahim, H., Wilusz, J. and Wilusz, C.J. (2008) RNA recognition by 30-to-5' exonucleases: the substrate perspective. Biochimica et Biophysica Acta., 1779, 256-265.
    • (2008) Biochimica et Biophysica Acta. , vol.1779 , pp. 256-265
    • Ibrahim, H.1    Wilusz, J.2    Wilusz, C.J.3
  • 36
    • 0026012161 scopus 로고
    • RNase T affects Escherichia coli growth and recovery from metabolic stress
    • Padmanabha, K.P. and Deutscher, M.P. (1991) RNase T affects Escherichia coli growth and recovery from metabolic stress. J. Bacteriol., 173, 1376-1381.
    • (1991) J. Bacteriol. , vol.173 , pp. 1376-1381
    • Padmanabha, K.P.1    Deutscher, M.P.2
  • 37
    • 0026666335 scopus 로고
    • The presence of only one of five exoribonucleases is sufficient to support the growth of Escherichia coli
    • Kelly, K.O. and Deutscher, M.P. (1992) The presence of only one of five exoribonucleases is sufficient to support the growth of Escherichia coli. J. Bacteriol., 174, 6682-6684.
    • (1992) J. Bacteriol. , vol.174 , pp. 6682-6684
    • Kelly, K.O.1    Deutscher, M.P.2
  • 38
    • 0033057293 scopus 로고    scopus 로고
    • Identification of RNase T as a high-copy suppressor of the UV sensitivity associated with single-strand DNA exonuclease deficiency in Escherichia coli
    • Viswanathan, M., Lanjuin, A. and Lovett, S.T. (1999) Identification of RNase T as a high-copy suppressor of the UV sensitivity associated with single-strand DNA exonuclease deficiency in Escherichia coli. Genetics, 151, 929-934.
    • (1999) Genetics , vol.151 , pp. 929-934
    • Viswanathan, M.1    Lanjuin, A.2    Lovett, S.T.3
  • 39
    • 0028100687 scopus 로고
    • The role of individual exoribonucleases in processing at the 30 end of Escherichia coli tRNA precursors
    • Li, Z. and Deutscher, M.P. (1994) The role of individual exoribonucleases in processing at the 30 end of Escherichia coli tRNA precursors. J. Biol. Chem., 269, 6064-6071.
    • (1994) J. Biol. Chem. , vol.269 , pp. 6064-6071
    • Li, Z.1    Deutscher, M.P.2
  • 40
    • 0034832844 scopus 로고    scopus 로고
    • This is the end: Processing editing and repair at the tRNA 30-terminus
    • Schurer, H., Schiffer, S., Marchfelder, A. and Morl, M. (2001) This is the end: processing, editing and repair at the tRNA 30-terminus. Biol. Chem., 382, 1147-1156.
    • (2001) Biol. Chem. , vol.382 , pp. 1147-1156
    • Schurer, H.1    Schiffer, S.2    Marchfelder, A.3    Morl, M.4
  • 41
    • 6944236106 scopus 로고    scopus 로고
    • TRNA maturation: RNA polymerization without a nucleic acid template
    • Weiner, A.M. (2004) tRNA maturation: RNA polymerization without a nucleic acid template. Curr. Biol., 14, R883-R885.
    • (2004) Curr. Biol. , vol.14
    • Weiner, A.M.1
  • 42
    • 0018077876 scopus 로고
    • Preparation of synthetic tRNA precursors with tRNA nucleotidyltransferase
    • Deutscher, M.P. and Ghosh, R.K. (1978) Preparation of synthetic tRNA precursors with tRNA nucleotidyltransferase. Nucleic Acids Res., 5, 3821-3829.
    • (1978) Nucleic Acids Res. , vol.5 , pp. 3821-3829
    • Deutscher, M.P.1    Ghosh, R.K.2
  • 43
    • 43449087645 scopus 로고    scopus 로고
    • TRNA integrity is a prerequisite for rapid CCA addition: Implication for quality control
    • Dupasquier, M., Kim, S., Halkidis, K., Gamper, H. and Hou, Y.M. (2008) tRNA integrity is a prerequisite for rapid CCA addition: implication for quality control. J. Mol. Biol., 379, 579-588.
    • (2008) J. Mol. Biol. , vol.379 , pp. 579-588
    • Dupasquier, M.1    Kim, S.2    Halkidis, K.3    Gamper, H.4    Hou, Y.M.5
  • 44
    • 77951129759 scopus 로고    scopus 로고
    • CCA addition to tRNA: Implications for tRNA quality control
    • Hou, Y.M. (2010) CCA addition to tRNA: implications for tRNA quality control. IUBMB life, 62, 251-260.
    • (2010) IUBMB Life , vol.62 , pp. 251-260
    • Hou, Y.M.1
  • 45
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe, T.M. and Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 46
    • 84856022000 scopus 로고    scopus 로고
    • Role of precursor sequences in the ordered maturation of E. coli 23S ribosomal RNA
    • Gutgsell, N.S. and Jain, C. (2012) Role of precursor sequences in the ordered maturation of E. coli 23S ribosomal RNA. RNA, 18, 345-353.
    • (2012) RNA , vol.18 , pp. 345-353
    • Gutgsell, N.S.1    Jain, C.2
  • 47
    • 2542487488 scopus 로고    scopus 로고
    • Functional interaction between RNase III and the Escherichia coli ribosome
    • Allas, U., Liiv, A. and Remme, J. (2003) Functional interaction between RNase III and the Escherichia coli ribosome. BMC Mol. Biol., 4, 8.
    • (2003) BMC Mol. Biol. , vol.4 , pp. 8
    • Allas, U.1    Liiv, A.2    Remme, J.3
  • 48
    • 33847042739 scopus 로고    scopus 로고
    • Protein-RNA interactions: Structural analysis and functional classes
    • Ellis, J.J., Broom, M. and Jones, S. (2007) Protein-RNA interactions: structural analysis and functional classes. Proteins, 66, 903-911.
    • (2007) Proteins , vol.66 , pp. 903-911
    • Ellis, J.J.1    Broom, M.2    Jones, S.3
  • 49
    • 0035393302 scopus 로고    scopus 로고
    • Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
    • Luscombe, N.M., Laskowski, R.A. and Thornton, J.M. (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res., 29, 2860-2874.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2860-2874
    • Luscombe, N.M.1    Laskowski, R.A.2    Thornton, J.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.