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Volumn 116, Issue 3, 2004, Pages 381-391

Structural basis for substrate selection by T7 RNA polymerase

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBOSE; RIBOSE; RNA POLYMERASE; TYROSINE;

EID: 1642276330     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(04)00059-5     Document Type: Article
Times cited : (172)

References (54)
  • 1
    • 0032584219 scopus 로고    scopus 로고
    • A single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides
    • Astatke M., Ng K., Grindley N.D., Joyce C.M. A single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides. Proc. Natl. Acad. Sci. USA. 95:1998;3402-3407.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 3402-3407
    • Astatke, M.1    Ng, K.2    Grindley, N.D.3    Joyce, C.M.4
  • 2
    • 0030906056 scopus 로고    scopus 로고
    • Base miscoding and strand misalignment errors by mutator Klenow polymerases with amino acid substitutions at tyrosine 766 in the O helix of the fingers subdomain
    • Bell J.B., Eckert K.A., Joyce C.M., Kunkel T.A. Base miscoding and strand misalignment errors by mutator Klenow polymerases with amino acid substitutions at tyrosine 766 in the O helix of the fingers subdomain. J. Biol. Chem. 272:1997;7345-7351.
    • (1997) J. Biol. Chem. , vol.272 , pp. 7345-7351
    • Bell, J.B.1    Eckert, K.A.2    Joyce, C.M.3    Kunkel, T.A.4
  • 3
    • 0026733634 scopus 로고
    • Mutations in T7 RNA polymerase that support the proposal for a common polymerase active site structure
    • Bonner G., Patra D., Lafer E.M., Sousa R. Mutations in T7 RNA polymerase that support the proposal for a common polymerase active site structure. EMBO J. 11:1992;3767-3775.
    • (1992) EMBO J. , vol.11 , pp. 3767-3775
    • Bonner, G.1    Patra, D.2    Lafer, E.M.3    Sousa, R.4
  • 4
    • 0028027513 scopus 로고
    • Characterization of a set of T7 RNA polymerase active site mutants
    • Bonner G., Lafer E.M., Sousa R. Characterization of a set of T7 RNA polymerase active site mutants. J. Biol. Chem. 269:1994;25120-25128.
    • (1994) J. Biol. Chem. , vol.269 , pp. 25120-25128
    • Bonner, G.1    Lafer, E.M.2    Sousa, R.3
  • 5
    • 0034620583 scopus 로고    scopus 로고
    • Roles of histidine 784 and tyrosine 639 in ribose discrimination by T7 RNA polymerase
    • Brieba L.G., Sousa R. Roles of histidine 784 and tyrosine 639 in ribose discrimination by T7 RNA polymerase. Biochemistry. 39:2000;919-923.
    • (2000) Biochemistry , vol.39 , pp. 919-923
    • Brieba, L.G.1    Sousa, R.2
  • 7
    • 0033579380 scopus 로고    scopus 로고
    • Structure of a transcribing T7 RNA polymerase initiation complex
    • Cheetham G.M., Steitz T.A. Structure of a transcribing T7 RNA polymerase initiation complex. Science. 286:1999;2305-2309.
    • (1999) Science , vol.286 , pp. 2305-2309
    • Cheetham, G.M.1    Steitz, T.A.2
  • 8
    • 0035827346 scopus 로고    scopus 로고
    • Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution
    • Cramer P., Bushnell D.A., Kornberg R.D. Structural basis of transcription. RNA polymerase II at 2.8 angstrom resolution Science. 292:2001;1863-1876.
    • (2001) Science , vol.292 , pp. 1863-1876
    • Cramer, P.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 10
    • 0032518398 scopus 로고    scopus 로고
    • Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
    • Doublie S., Tabor S., Long A.M., Richardson C.C., Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature. 391:1998;251-258.
    • (1998) Nature , vol.391 , pp. 251-258
    • Doublie, S.1    Tabor, S.2    Long, A.M.3    Richardson, C.C.4    Ellenberger, T.5
  • 12
    • 0033119938 scopus 로고    scopus 로고
    • Further additions to MolScript version 1.4, including reading and contouring of electron-density maps
    • Esnouf R.M. Further additions to MolScript version 1.4, including reading and contouring of electron-density maps. Acta Crystallogr. D. 55:1999;938-940.
    • (1999) Acta Crystallogr. D , vol.55 , pp. 938-940
    • Esnouf, R.M.1
  • 13
    • 0035958552 scopus 로고    scopus 로고
    • Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation
    • Foster J.E., Holmes S.F., Erie D.A. Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation. Cell. 106:2001;243-252.
    • (2001) Cell , vol.106 , pp. 243-252
    • Foster, J.E.1    Holmes, S.F.2    Erie, D.A.3
  • 14
    • 0035827332 scopus 로고    scopus 로고
    • Structural basis of transcription: An RNA polymerase II elongation complex at 3.3 Å resolution
    • Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D. Structural basis of transcription. an RNA polymerase II elongation complex at 3.3 Å resolution Science. 292:2001;1876-1882.
    • (2001) Science , vol.292 , pp. 1876-1882
    • Gnatt, A.L.1    Cramer, P.2    Fu, J.3    Bushnell, D.A.4    Kornberg, R.D.5
  • 15
    • 0031561795 scopus 로고    scopus 로고
    • A model for the mechanism of polymerase translocation
    • Guajardo R., Sousa R. A model for the mechanism of polymerase translocation. J. Mol. Biol. 265:1997;8-19.
    • (1997) J. Mol. Biol. , vol.265 , pp. 8-19
    • Guajardo, R.1    Sousa, R.2
  • 16
    • 0041315524 scopus 로고    scopus 로고
    • Downstream DNA sequence effects on transcription elongation. Allosteric binding of nucleoside triphosphates facilitates translocation via a ratchet motion
    • Holmes S.F., Erie D.A. Downstream DNA sequence effects on transcription elongation. Allosteric binding of nucleoside triphosphates facilitates translocation via a ratchet motion. J. Biol. Chem. 278:2003;35597-35608.
    • (2003) J. Biol. Chem. , vol.278 , pp. 35597-35608
    • Holmes, S.F.1    Erie, D.A.2
  • 17
    • 0034721946 scopus 로고    scopus 로고
    • T7 RNA polymerase elongation complex structure and movement
    • Huang J., Sousa R. T7 RNA polymerase elongation complex structure and movement. J. Mol. Biol. 303:2000;347-358.
    • (2000) J. Mol. Biol. , vol.303 , pp. 347-358
    • Huang, J.1    Sousa, R.2
  • 18
    • 0034718567 scopus 로고    scopus 로고
    • Misincorporation by wild-type and mutant T7 RNA polymerases: Identification of interactions that reduce misincorporation rates by stabilizing the catalytically incompetent open conformation
    • Huang J., Brieba L.G., Sousa R. Misincorporation by wild-type and mutant T7 RNA polymerases. identification of interactions that reduce misincorporation rates by stabilizing the catalytically incompetent open conformation Biochemistry. 39:2000;11571-11580.
    • (2000) Biochemistry , vol.39 , pp. 11571-11580
    • Huang, J.1    Brieba, L.G.2    Sousa, R.3
  • 19
    • 0030727136 scopus 로고    scopus 로고
    • Determinants of ribose specificity in RNA polymerization: Effects of Mn2+ and deoxynucleoside monophosphate incorporation into transcripts
    • a
    • Huang Y., Beaudry A., McSwiggen J., Sousa R. Determinants of ribose specificity in RNA polymerization. effects of Mn2+ and deoxynucleoside monophosphate incorporation into transcripts Biochemistry. 36:1997;13718-13728. a.
    • (1997) Biochemistry , vol.36 , pp. 13718-13728
    • Huang, Y.1    Beaudry, A.2    McSwiggen, J.3    Sousa, R.4
  • 20
    • 0030854581 scopus 로고    scopus 로고
    • Mechanism of ribose 2′-group discrimination by an RNA polymerase
    • b
    • Huang Y., Eckstein F., Padilla R., Sousa R. Mechanism of ribose 2′-group discrimination by an RNA polymerase. Biochemistry. 36:1997;8231-8242. b.
    • (1997) Biochemistry , vol.36 , pp. 8231-8242
    • Huang, Y.1    Eckstein, F.2    Padilla, R.3    Sousa, R.4
  • 21
    • 0032527832 scopus 로고    scopus 로고
    • Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme
    • Jeruzalmi D., Steitz T.A. Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme. EMBO J. 17:1998;4101-4113.
    • (1998) EMBO J. , vol.17 , pp. 4101-4113
    • Jeruzalmi, D.1    Steitz, T.A.2
  • 22
    • 0037388383 scopus 로고    scopus 로고
    • Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations
    • Johnson S.J., Taylor J.S., Beese L.S. Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc. Natl. Acad. Sci. USA. 100:2003;3895-3900.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 3895-3900
    • Johnson, S.J.1    Taylor, J.S.2    Beese, L.S.3
  • 23
    • 0031042722 scopus 로고    scopus 로고
    • Choosing the right sugar: How polymerases select a nucleotide substrate
    • Joyce C.M. Choosing the right sugar. how polymerases select a nucleotide substrate Proc. Natl. Acad. Sci. USA. 94:1997;1619-1622.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 1619-1622
    • Joyce, C.M.1
  • 25
    • 0032518524 scopus 로고    scopus 로고
    • Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
    • Kiefer J.R., Mao C., Braman J.C., Beese L.S. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature. 391:1998;304-307.
    • (1998) Nature , vol.391 , pp. 304-307
    • Kiefer, J.R.1    Mao, C.2    Braman, J.C.3    Beese, L.S.4
  • 27
    • 0026244229 scopus 로고
    • Molscript: A program to produce both detailed and schematic plots of protein structures
    • Kraulis P.J. Molscript. a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallogr. 24:1991;946-950.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 28
    • 0031861823 scopus 로고    scopus 로고
    • Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates
    • a
    • Li Y., Kong Y., Korolev S., Waksman G. Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates. Protein Sci. 7:1998;1116-1123. a.
    • (1998) Protein Sci. , vol.7 , pp. 1116-1123
    • Li, Y.1    Kong, Y.2    Korolev, S.3    Waksman, G.4
  • 29
    • 0032535528 scopus 로고    scopus 로고
    • Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation
    • b
    • Li Y., Korolev S., Waksman G. Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I. structural basis for nucleotide incorporation EMBO J. 17:1998;7514-7525. b.
    • (1998) EMBO J. , vol.17 , pp. 7514-7525
    • Li, Y.1    Korolev, S.2    Waksman, G.3
  • 30
    • 0037044758 scopus 로고    scopus 로고
    • Major conformational changes occur during the transition from an initiation complex to an elongation complex by T7 RNA polymerase
    • Ma K., Temiakov D., Jiang M., Anikin M., McAllister W.T. Major conformational changes occur during the transition from an initiation complex to an elongation complex by T7 RNA polymerase. J. Biol. Chem. 277:2002;43206-43215.
    • (2002) J. Biol. Chem. , vol.277 , pp. 43206-43215
    • Ma, K.1    Temiakov, D.2    Jiang, M.3    Anikin, M.4    McAllister, W.T.5
  • 31
    • 0003367846 scopus 로고    scopus 로고
    • Transcription by T7 RNA polymerase
    • McAllister W.T. Transcription by T7 RNA polymerase. Nucl. Acids Mol. Biol. 11:1997;15-25.
    • (1997) Nucl. Acids Mol. Biol. , vol.11 , pp. 15-25
    • McAllister, W.T.1
  • 32
    • 0027508119 scopus 로고
    • The phage RNA polymerases are related to DNA polymerases and reverse transcriptases
    • McAllister W.T., Raskin C.A. The phage RNA polymerases are related to DNA polymerases and reverse transcriptases. Mol. Microbiol. 10:1993;1-6.
    • (1993) Mol. Microbiol. , vol.10 , pp. 1-6
    • McAllister, W.T.1    Raskin, C.A.2
  • 33
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: Photorealistic molecular graphics
    • Merrit E.A., Bacon D.J. Raster3D. photorealistic molecular graphics Methods Enzymol. 277:1997;505-524.
    • (1997) Methods Enzymol. , vol.277 , pp. 505-524
    • Merrit, E.A.1    Bacon, D.J.2
  • 34
    • 0033613841 scopus 로고    scopus 로고
    • Side chains that influence fidelity at the polymerase active site of Escherichia coli DNA polymerase I (Klenow fragment)
    • Minnick D.T., Bebenek K., Osheroff W.P., Turner R.M. Jr., Astatke M., Liu L., Kunkel T.A., Joyce C.M. Side chains that influence fidelity at the polymerase active site of Escherichia coli DNA polymerase I (Klenow fragment). J. Biol. Chem. 274:1999;3067-3075.
    • (1999) J. Biol. Chem. , vol.274 , pp. 3067-3075
    • Minnick, D.T.1    Bebenek, K.2    Osheroff, W.P.3    Turner, R.M.Jr.4    Astatke, M.5    Liu, L.6    Kunkel, T.A.7    Joyce, C.M.8
  • 35
    • 0037022239 scopus 로고    scopus 로고
    • Discrimination against purine-pyrimidine mispairs in the polymerase active site of DNA polymerase I: A structural explanation
    • Minnick D.T., Liu L., Grindley N.D., Kunkel T.A., Joyce C.M. Discrimination against purine-pyrimidine mispairs in the polymerase active site of DNA polymerase I. a structural explanation Proc. Natl. Acad. Sci. USA. 99:2002;1194-1199.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 1194-1199
    • Minnick, D.T.1    Liu, L.2    Grindley, N.D.3    Kunkel, T.A.4    Joyce, C.M.5
  • 37
    • 0026763294 scopus 로고
    • Asp537, Asp812 are essential and Lys631, His811 are catalytically significant in bacteriophage T7 RNA polymerase activity
    • Osumi-Davis P.A., de Aguilera M.C., Woody R.W., Woody A.Y. Asp537, Asp812 are essential and Lys631, His811 are catalytically significant in bacteriophage T7 RNA polymerase activity. J. Mol. Biol. 226:1992;37-45.
    • (1992) J. Mol. Biol. , vol.226 , pp. 37-45
    • Osumi-Davis, P.A.1    De Aguilera, M.C.2    Woody, R.W.3    Woody, A.Y.4
  • 38
    • 0031059866 scopus 로고    scopus 로고
    • Processing X-ray diffraction data collected in oscillation mode
    • Otwinowski Z., Minor W. Processing 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
  • 39
    • 0035906661 scopus 로고    scopus 로고
    • Prokaryotic DNA polymerase I: Evolution, structure, and "base flipping" mechanism for nucleotide selection
    • Patel P.H., Suzuki M., Adman E., Shinkai A., Loeb L.A. Prokaryotic DNA polymerase I. evolution, structure, and "base flipping" mechanism for nucleotide selection J. Mol. Biol. 308:2001;823-837.
    • (2001) J. Mol. Biol. , vol.308 , pp. 823-837
    • Patel, P.H.1    Suzuki, M.2    Adman, E.3    Shinkai, A.4    Loeb, L.A.5
  • 40
    • 0035861641 scopus 로고    scopus 로고
    • In vivo mutagenesis by Escherichia coli DNA polymerase I. Ile(709) in motif a functions in base selection
    • Shinkai A., Loeb L.A. In vivo mutagenesis by Escherichia coli DNA polymerase I. Ile(709) in motif A functions in base selection. J. Biol. Chem. 276:2001;46759-46764.
    • (2001) J. Biol. Chem. , vol.276 , pp. 46759-46764
    • Shinkai, A.1    Loeb, L.A.2
  • 41
    • 0029091457 scopus 로고
    • A mutant T7 RNA polymerase as a DNA polymerase
    • Sousa R., Padilla R. A mutant T7 RNA polymerase as a DNA polymerase. EMBO J. 14:1995;4609-4621.
    • (1995) EMBO J. , vol.14 , pp. 4609-4621
    • Sousa, R.1    Padilla, R.2
  • 42
    • 0027163526 scopus 로고
    • Crystal structure of bacteriophage T7 RNA polymerase at 3.3 Å resolution
    • Sousa R., Chung Y.J., Rose J.P., Wang B.C. Crystal structure of bacteriophage T7 RNA polymerase at 3.3 Å resolution. Nature. 364:1993;593-599.
    • (1993) Nature , vol.364 , pp. 593-599
    • Sousa, R.1    Chung, Y.J.2    Rose, J.P.3    Wang, B.C.4
  • 43
    • 0027184481 scopus 로고
    • A general two-metal-ion mechanism for catalytic RNA
    • Steitz T.A., Steitz J.A. A general two-metal-ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci. USA. 90:1993;6498-6502.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 6498-6502
    • Steitz, T.A.1    Steitz, J.A.2
  • 44
    • 0028606031 scopus 로고
    • A unified polymerase mechanism for nonhomologous DNA and RNA polymerases
    • Steitz T.A., Smerdon S.J., Jager J., Joyce C.M. A unified polymerase mechanism for nonhomologous DNA and RNA polymerases. Science. 266:1994;2022-2025.
    • (1994) Science , vol.266 , pp. 2022-2025
    • Steitz, T.A.1    Smerdon, S.J.2    Jager, J.3    Joyce, C.M.4
  • 46
    • 0037033076 scopus 로고    scopus 로고
    • Characterization of T7 RNA polymerase transcription complexes assembled on nucleic acid scaffolds
    • Temiakov D., Anikin M., McAllister W.T. Characterization of T7 RNA polymerase transcription complexes assembled on nucleic acid scaffolds. J. Biol. Chem. 277:2002;47035-47043.
    • (2002) J. Biol. Chem. , vol.277 , pp. 47035-47043
    • Temiakov, D.1    Anikin, M.2    McAllister, W.T.3
  • 47
    • 0034687683 scopus 로고    scopus 로고
    • The specificity loop of T7 RNA polymerase interacts first with the promoter and then with the elongating transcript, suggesting a mechanism for promoter clearance
    • Temiakov D., Mentesana P.E., Ma K., Mustaev A., Borukhov S., McAllister W.T. The specificity loop of T7 RNA polymerase interacts first with the promoter and then with the elongating transcript, suggesting a mechanism for promoter clearance. Proc. Natl. Acad. Sci. USA. 97:2000;14109-14114.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 14109-14114
    • Temiakov, D.1    Mentesana, P.E.2    Ma, K.3    Mustaev, A.4    Borukhov, S.5    McAllister, W.T.6
  • 49
    • 0035920224 scopus 로고    scopus 로고
    • O-helix mutant T664P of Thermus aquaticus DNA polymerase I: Altered catalytic properties for incorporation of incorrect nucleotides but not correct nucleotides
    • Tosaka A., Ogawa M., Yoshida S., Suzuki M. O-helix mutant T664P of Thermus aquaticus DNA polymerase I. altered catalytic properties for incorporation of incorrect nucleotides but not correct nucleotides J. Biol. Chem. 276:2001;27562-27567.
    • (2001) J. Biol. Chem. , vol.276 , pp. 27562-27567
    • Tosaka, A.1    Ogawa, M.2    Yoshida, S.3    Suzuki, M.4
  • 50
    • 0036817892 scopus 로고    scopus 로고
    • Structural-functional analysis of bacteriophage T7 RNA polymerase
    • Tunitskaya V.L., Kochetkov S.N. Structural-functional analysis of bacteriophage T7 RNA polymerase. Biochemistry (Moscow). 67:2002;1124-1135.
    • (2002) Biochemistry (Moscow) , vol.67 , pp. 1124-1135
    • Tunitskaya, V.L.1    Kochetkov, S.N.2
  • 52
    • 0032506259 scopus 로고    scopus 로고
    • Pre-steady-state and steady-state kinetic studies on transcription initiation catalyzed by T7 RNA polymerase and its active-site mutants K631R and Y639F
    • Woody A.Y., Osumi-Davis P.A., Hiremath M.M., Woody R.W. Pre-steady-state and steady-state kinetic studies on transcription initiation catalyzed by T7 RNA polymerase and its active-site mutants K631R and Y639F. Biochemistry. 37:1998;15958-15964.
    • (1998) Biochemistry , vol.37 , pp. 15958-15964
    • Woody, A.Y.1    Osumi-Davis, P.A.2    Hiremath, M.M.3    Woody, R.W.4
  • 53
    • 0037112082 scopus 로고    scopus 로고
    • Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase
    • Yin Y.W., Steitz T.A. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science. 298:2002;1387-1395.
    • (2002) Science , vol.298 , pp. 1387-1395
    • Yin, Y.W.1    Steitz, T.A.2
  • 54
    • 1342313235 scopus 로고    scopus 로고
    • The mechanism of translocation and helicase activity in T7 RNA polymerase
    • , this issue
    • Yin W.Y., Steitz T.A. The mechanism of translocation and helicase activity in T7 RNA polymerase. Cell. 116:2004;393-404., this issue.
    • (2004) Cell , vol.116 , pp. 393-404
    • Yin, W.Y.1    Steitz, T.A.2


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