-
1
-
-
0032518374
-
A mechanism for all polymerases
-
10.1038/34542, 9440683
-
Steitz TA. A mechanism for all polymerases. Nature 1998, 391:231-232. 10.1038/34542, 9440683.
-
(1998)
Nature
, vol.391
, pp. 231-232
-
-
Steitz, T.A.1
-
2
-
-
0027184481
-
A general two-metal-ion mechanism for catalytic RNA
-
10.1073/pnas.90.14.6498, 46959, 8341661
-
Steitz TA, Steitz JA. A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 1993, 90:6498-6502. 10.1073/pnas.90.14.6498, 46959, 8341661.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 6498-6502
-
-
Steitz, T.A.1
Steitz, J.A.2
-
3
-
-
0037543997
-
Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase
-
10.1093/emboj/cdg193, 156065, 12727889
-
Sosunov V, Sosunova E, Mustaev A, Bass I, Nikiforov V, Goldfarb A. Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase. Embo J 2003, 22:2234-2244. 10.1093/emboj/cdg193, 156065, 12727889.
-
(2003)
Embo J
, vol.22
, pp. 2234-2244
-
-
Sosunov, V.1
Sosunova, E.2
Mustaev, A.3
Bass, I.4
Nikiforov, V.5
Goldfarb, A.6
-
4
-
-
22844436748
-
The involvement of the aspartate triad of the active center in all catalytic activities of multisubunit RNA polymerase
-
10.1093/nar/gki688, 1180743, 16049026
-
Sosunov V, Zorov S, Sosunova E, Nikolaev A, Zakeyeva I, Bass I, Goldfarb A, Nikiforov V, Severinov K, Mustaev A. The involvement of the aspartate triad of the active center in all catalytic activities of multisubunit RNA polymerase. Nucleic Acids Res 2005, 33:4202-4211. 10.1093/nar/gki688, 1180743, 16049026.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 4202-4211
-
-
Sosunov, V.1
Zorov, S.2
Sosunova, E.3
Nikolaev, A.4
Zakeyeva, I.5
Bass, I.6
Goldfarb, A.7
Nikiforov, V.8
Severinov, K.9
Mustaev, A.10
-
5
-
-
57249108333
-
Bridge helix and trigger loop perturbations generate superactive RNA polymerases
-
10.1186/jbiol98, 2776397, 19055851
-
Tan L, Wiesler S, Trzaska D, Carney HC, Weinzierl RO. Bridge helix and trigger loop perturbations generate superactive RNA polymerases. J Biol 2008, 7:40. 10.1186/jbiol98, 2776397, 19055851.
-
(2008)
J Biol
, vol.7
, pp. 40
-
-
Tan, L.1
Wiesler, S.2
Trzaska, D.3
Carney, H.C.4
Weinzierl, R.O.5
-
6
-
-
44449094019
-
Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation
-
10.1016/j.molcel.2008.04.017, 18538654
-
Kireeva ML, Nedialkov YA, Cremona GH, Purtov YA, Lubkowska L, Malagon F, Burton ZF, Strathern JN, Kashlev M. Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. Mol Cell 2008, 30:557-566. 10.1016/j.molcel.2008.04.017, 18538654.
-
(2008)
Mol Cell
, vol.30
, pp. 557-566
-
-
Kireeva, M.L.1
Nedialkov, Y.A.2
Cremona, G.H.3
Purtov, Y.A.4
Lubkowska, L.5
Malagon, F.6
Burton, Z.F.7
Strathern, J.N.8
Kashlev, M.9
-
7
-
-
24044497229
-
Structural basis of transcription inhibition by antibiotic streptolydigin
-
10.1016/j.molcel.2005.07.020, 16167380
-
Temiakov D, Zenkin N, Vassylyeva MN, Perederina A, Tahirov TH, Kashkina E, Savkina M, Zorov S, Nikiforov V, Igarashi N, Matsugaki N, Wakatsuki S, Severinov K, Vassylyev DG. Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell 2005, 19:655-666. 10.1016/j.molcel.2005.07.020, 16167380.
-
(2005)
Mol Cell
, vol.19
, pp. 655-666
-
-
Temiakov, D.1
Zenkin, N.2
Vassylyeva, M.N.3
Perederina, A.4
Tahirov, T.H.5
Kashkina, E.6
Savkina, M.7
Zorov, S.8
Nikiforov, V.9
Igarashi, N.10
Matsugaki, N.11
Wakatsuki, S.12
Severinov, K.13
Vassylyev, D.G.14
-
8
-
-
10944232674
-
Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS
-
10.1016/j.molcel.2004.11.040, 15610738
-
Kettenberger H, Armache KJ, Cramer P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell 2004, 16:955-965. 10.1016/j.molcel.2004.11.040, 15610738.
-
(2004)
Mol Cell
, vol.16
, pp. 955-965
-
-
Kettenberger, H.1
Armache, K.J.2
Cramer, P.3
-
9
-
-
34447513771
-
Structural basis for substrate loading in bacterial RNA polymerase
-
10.1038/nature05931, 17581591
-
Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R. Structural basis for substrate loading in bacterial RNA polymerase. Nature 2007, 448:163-168. 10.1038/nature05931, 17581591.
-
(2007)
Nature
, vol.448
, pp. 163-168
-
-
Vassylyev, D.G.1
Vassylyeva, M.N.2
Zhang, J.3
Palangat, M.4
Artsimovitch, I.5
Landick, R.6
-
10
-
-
44449103640
-
The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin
-
Kaplan CD, Larsson KM, Kornberg RD. The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin. Mol Cell 2008, 30:47-556.
-
(2008)
Mol Cell
, vol.30
, pp. 47-556
-
-
Kaplan, C.D.1
Larsson, K.M.2
Kornberg, R.D.3
-
11
-
-
33751235874
-
Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis
-
10.1016/j.cell.2006.11.023, 1876690, 17129781
-
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 2006, 127:941-954. 10.1016/j.cell.2006.11.023, 1876690, 17129781.
-
(2006)
Cell
, vol.127
, pp. 941-954
-
-
Wang, D.1
Bushnell, D.A.2
Westover, K.D.3
Kaplan, C.D.4
Kornberg, R.D.5
-
12
-
-
59649110607
-
Nucleic acid polymerases use a general acid for nucleotidyl transfer
-
10.1038/nsmb.1540, 2728625, 19151724
-
Castro C, Smidansky ED, Arnold JJ, Maksimchuk KR, Moustafa I, Uchida A, Gotte M, Konigsberg W, Cameron CE. Nucleic acid polymerases use a general acid for nucleotidyl transfer. Nat Struct Mol Biol 2009, 16:212-218. 10.1038/nsmb.1540, 2728625, 19151724.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 212-218
-
-
Castro, C.1
Smidansky, E.D.2
Arnold, J.J.3
Maksimchuk, K.R.4
Moustafa, I.5
Uchida, A.6
Gotte, M.7
Konigsberg, W.8
Cameron, C.E.9
-
13
-
-
77449093660
-
Role of the RNA polymerase trigger loop in catalysis and pausing
-
10.1038/nsmb.1732, 19966797
-
Zhang J, Palangat M, Landick R. Role of the RNA polymerase trigger loop in catalysis and pausing. Nat Struct Mol Biol 2009, 17:99-104. 10.1038/nsmb.1732, 19966797.
-
(2009)
Nat Struct Mol Biol
, vol.17
, pp. 99-104
-
-
Zhang, J.1
Palangat, M.2
Landick, R.3
-
14
-
-
12944324227
-
A ratchet mechanism of transcription elongation and its control
-
10.1016/j.cell.2004.11.045, 15680325
-
Bar-Nahum G, Epshtein V, Ruckenstein AE, Rafikov R, Mustaev A, Nudler E. A ratchet mechanism of transcription elongation and its control. Cell 2005, 120:183-193. 10.1016/j.cell.2004.11.045, 15680325.
-
(2005)
Cell
, vol.120
, pp. 183-193
-
-
Bar-Nahum, G.1
Epshtein, V.2
Ruckenstein, A.E.3
Rafikov, R.4
Mustaev, A.5
Nudler, E.6
-
15
-
-
33746634704
-
Transcript-assisted transcriptional proofreading
-
10.1126/science.1127422, 16873663
-
Zenkin N, Yuzenkova Y, Severinov K. Transcript-assisted transcriptional proofreading. Science 2006, 313:518-520. 10.1126/science.1127422, 16873663.
-
(2006)
Science
, vol.313
, pp. 518-520
-
-
Zenkin, N.1
Yuzenkova, Y.2
Severinov, K.3
-
16
-
-
0032113494
-
Crucial role of the RNA:DNA hybrid in the processivity of transcription
-
10.1016/S1097-2765(00)80113-6, 9702191
-
Sidorenkov I, Komissarova N, Kashlev M. Crucial role of the RNA:DNA hybrid in the processivity of transcription. Mol Cell 1998, 2:55-64. 10.1016/S1097-2765(00)80113-6, 9702191.
-
(1998)
Mol Cell
, vol.2
, pp. 55-64
-
-
Sidorenkov, I.1
Komissarova, N.2
Kashlev, M.3
-
17
-
-
34547204502
-
A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing
-
10.1016/j.molcel.2007.06.008, 17679091
-
Toulokhonov I, Zhang J, Palangat M, Landick R. A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. Mol Cell 2007, 27:406-419. 10.1016/j.molcel.2007.06.008, 17679091.
-
(2007)
Mol Cell
, vol.27
, pp. 406-419
-
-
Toulokhonov, I.1
Zhang, J.2
Palangat, M.3
Landick, R.4
-
18
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
10.1006/jmbi.1999.2700, 10329189
-
Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999, 288:911-940. 10.1006/jmbi.1999.2700, 10329189.
-
(1999)
J Mol Biol
, vol.288
, pp. 911-940
-
-
Mathews, D.H.1
Sabina, J.2
Zuker, M.3
Turner, D.H.4
-
19
-
-
4644265121
-
Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase
-
10.1074/jbc.C400316200, 15262972
-
Svetlov V, Vassylyev DG, Artsimovitch I. Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase. J Biol Chem 2004, 279:38087-38090. 10.1074/jbc.C400316200, 15262972.
-
(2004)
J Biol Chem
, vol.279
, pp. 38087-38090
-
-
Svetlov, V.1
Vassylyev, D.G.2
Artsimovitch, I.3
-
20
-
-
0028820262
-
Primer synthesis kinetics by Escherichia coli primase on single-stranded DNA templates
-
10.1021/bi00049a025, 8519767
-
Swart JR, Griep MA. Primer synthesis kinetics by Escherichia coli primase on single-stranded DNA templates. Biochemistry 1995, 34:16097-16106. 10.1021/bi00049a025, 8519767.
-
(1995)
Biochemistry
, vol.34
, pp. 16097-16106
-
-
Swart, J.R.1
Griep, M.A.2
-
21
-
-
0034912668
-
DNA primases
-
10.1146/annurev.biochem.70.1.39, 11395402
-
Frick DN, Richardson CC. DNA primases. Annu Rev Biochem 2001, 70:39-80. 10.1146/annurev.biochem.70.1.39, 11395402.
-
(2001)
Annu Rev Biochem
, vol.70
, pp. 39-80
-
-
Frick, D.N.1
Richardson, C.C.2
-
22
-
-
0033782798
-
DNA replication fidelity
-
10.1146/annurev.biochem.69.1.497, 10966467
-
Kunkel TA, Bebenek K. DNA replication fidelity. Annu Rev Biochem 2000, 69:497-529. 10.1146/annurev.biochem.69.1.497, 10966467.
-
(2000)
Annu Rev Biochem
, vol.69
, pp. 497-529
-
-
Kunkel, T.A.1
Bebenek, K.2
-
23
-
-
1642276330
-
Structural basis for substrate selection by t7 RNA polymerase
-
10.1016/S0092-8674(04)00059-5, 15016373
-
Temiakov D, Patlan V, Anikin M, McAllister WT, Yokoyama S, Vassylyev DG. Structural basis for substrate selection by t7 RNA polymerase. Cell 2004, 116:381-391. 10.1016/S0092-8674(04)00059-5, 15016373.
-
(2004)
Cell
, vol.116
, pp. 381-391
-
-
Temiakov, D.1
Patlan, V.2
Anikin, M.3
McAllister, W.T.4
Yokoyama, S.5
Vassylyev, D.G.6
-
24
-
-
67449116330
-
Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA
-
10.1016/j.molcel.2009.06.002, 19560423
-
Sydow JF, Brueckner F, Cheung AC, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P. Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Mol Cell 2009, 34:710-721. 10.1016/j.molcel.2009.06.002, 19560423.
-
(2009)
Mol Cell
, vol.34
, pp. 710-721
-
-
Sydow, J.F.1
Brueckner, F.2
Cheung, A.C.3
Damsma, G.E.4
Dengl, S.5
Lehmann, E.6
Vassylyev, D.7
Cramer, P.8
-
25
-
-
3142733093
-
Transcriptional fidelity and proofreading in Archaea and implications for the mechanism of TFS-induced RNA cleavage
-
10.1111/j.1365-2958.2004.04039.x, 15130130
-
Lange U, Hausner W. Transcriptional fidelity and proofreading in Archaea and implications for the mechanism of TFS-induced RNA cleavage. Mol Microbiol 2004, 52:1133-1143. 10.1111/j.1365-2958.2004.04039.x, 15130130.
-
(2004)
Mol Microbiol
, vol.52
, pp. 1133-1143
-
-
Lange, U.1
Hausner, W.2
-
26
-
-
0032524661
-
Transcriptional fidelity and proofreading by RNA polymerase II
-
10.1016/S0092-8674(00)81191-5, 9604937
-
Thomas MJ, Platas AA, Hawley DK. Transcriptional fidelity and proofreading by RNA polymerase II. Cell 1998, 93:627-637. 10.1016/S0092-8674(00)81191-5, 9604937.
-
(1998)
Cell
, vol.93
, pp. 627-637
-
-
Thomas, M.J.1
Platas, A.A.2
Hawley, D.K.3
-
27
-
-
0027761137
-
Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription
-
10.1126/science.8235608, 8235608
-
Erie DA, Hajiseyedjavadi O, Young MC, von Hippel PH. Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription. Science 1993, 262:867-873. 10.1126/science.8235608, 8235608.
-
(1993)
Science
, vol.262
, pp. 867-873
-
-
Erie, D.A.1
Hajiseyedjavadi, O.2
Young, M.C.3
von Hippel, P.H.4
-
28
-
-
33646188087
-
Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil
-
10.1534/genetics.105.052415, 1456368, 16510790
-
Malagon F, Kireeva ML, Shafer BK, Lubkowska L, Kashlev M, Strathern JN. Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil. Genetics 2006, 172:2201-2209. 10.1534/genetics.105.052415, 1456368, 16510790.
-
(2006)
Genetics
, vol.172
, pp. 2201-2209
-
-
Malagon, F.1
Kireeva, M.L.2
Shafer, B.K.3
Lubkowska, L.4
Kashlev, M.5
Strathern, J.N.6
-
29
-
-
33644976966
-
Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors
-
10.1074/jbc.C500405200, 1373684, 16298991
-
Symersky J, Perederina A, Vassylyeva MN, Svetlov V, Artsimovitch I, Vassylyev DG. Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors. J Biol Chem 2006, 281:1309-1312. 10.1074/jbc.C500405200, 1373684, 16298991.
-
(2006)
J Biol Chem
, vol.281
, pp. 1309-1312
-
-
Symersky, J.1
Perederina, A.2
Vassylyeva, M.N.3
Svetlov, V.4
Artsimovitch, I.5
Vassylyev, D.G.6
-
30
-
-
73149106601
-
Allosteric control of catalysis by the F loop of RNA polymerase
-
10.1073/pnas.0905402106, 2776430, 19855007
-
Miropolskaya N, Artsimovitch I, Klimasauskas S, Nikiforov V, Kulbachinskiy A. Allosteric control of catalysis by the F loop of RNA polymerase. Proc Natl Acad Sci USA 2009, 106:18942-19847. 10.1073/pnas.0905402106, 2776430, 19855007.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 18942-19847
-
-
Miropolskaya, N.1
Artsimovitch, I.2
Klimasauskas, S.3
Nikiforov, V.4
Kulbachinskiy, A.5
-
31
-
-
0347381303
-
Preparation and characterization of recombinant Thermus aquaticus RNA polymerase
-
full_text, 14712637
-
Kuznedelov K, Minakhin L, Severinov K. Preparation and characterization of recombinant Thermus aquaticus RNA polymerase. Methods Enzymol 2003, 370:94-108. full_text, 14712637.
-
(2003)
Methods Enzymol
, vol.370
, pp. 94-108
-
-
Kuznedelov, K.1
Minakhin, L.2
Severinov, K.3
-
32
-
-
0346890209
-
Mutations of bacterial RNA polymerase leading to resistance to microcin j25
-
10.1074/jbc.M209425200, 12401787
-
Yuzenkova J, Delgado M, Nechaev S, Savalia D, Epshtein V, Artsimovitch I, Mooney RA, Landick R, Farias RN, Salomon R, Severinov K. Mutations of bacterial RNA polymerase leading to resistance to microcin j25. J Biol Chem 2002, 277:50867-50875. 10.1074/jbc.M209425200, 12401787.
-
(2002)
J Biol Chem
, vol.277
, pp. 50867-50875
-
-
Yuzenkova, J.1
Delgado, M.2
Nechaev, S.3
Savalia, D.4
Epshtein, V.5
Artsimovitch, I.6
Mooney, R.A.7
Landick, R.8
Farias, R.N.9
Salomon, R.10
Severinov, K.11
-
33
-
-
0029809303
-
Histidine-tagged RNA polymerase of Escherichia coli and transcription in solid phase
-
full_text, 8902816
-
Kashlev M, Nudler E, Severinov K, Borukhov S, Komissarova N, Goldfarb A. Histidine-tagged RNA polymerase of Escherichia coli and transcription in solid phase. Methods Enzymol 1996, 274:326-334. full_text, 8902816.
-
(1996)
Methods Enzymol
, vol.274
, pp. 326-334
-
-
Kashlev, M.1
Nudler, E.2
Severinov, K.3
Borukhov, S.4
Komissarova, N.5
Goldfarb, A.6
-
35
-
-
0034266683
-
Stochastic ranking for constrained evolutionary optimization
-
Runnarson TP, Yao X. Stochastic ranking for constrained evolutionary optimization. IEEE Trans Evolutionary Computation 2000, 4:284-294.
-
(2000)
IEEE Trans Evolutionary Computation
, vol.4
, pp. 284-294
-
-
Runnarson, T.P.1
Yao, X.2
|