-
1
-
-
34548382114
-
Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis
-
Balbo P.B., and Bohm A. Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis. Structure 15 (2007) 1117-1131
-
(2007)
Structure
, vol.15
, pp. 1117-1131
-
-
Balbo, P.B.1
Bohm, A.2
-
2
-
-
19644361850
-
Kinetic studies of yeast polyA polymerase indicate an induced fit mechanism for nucleotide specificity
-
Balbo P.B., Meinke G., and Bohm A. Kinetic studies of yeast polyA polymerase indicate an induced fit mechanism for nucleotide specificity. Biochemistry 44 (2005) 7777-7786
-
(2005)
Biochemistry
, vol.44
, pp. 7777-7786
-
-
Balbo, P.B.1
Meinke, G.2
Bohm, A.3
-
3
-
-
33846781442
-
X-Ray crystallographic and steady state fluorescence characterization of the protein dynamics of yeast polyadenylate polymerase
-
Balbo P.B., Toth J., and Bohm A. X-Ray crystallographic and steady state fluorescence characterization of the protein dynamics of yeast polyadenylate polymerase. J. Mol. Biol. 366 (2007) 1401-1415
-
(2007)
J. Mol. Biol.
, vol.366
, pp. 1401-1415
-
-
Balbo, P.B.1
Toth, J.2
Bohm, A.3
-
4
-
-
0034714329
-
Structure of yeast poly(A) polymerase alone and in complex with 3′-dATP
-
Bard J., Zhelkovsky A.M., Helmling S., Earnest T.N., Moore C.L., and Bohm A. Structure of yeast poly(A) polymerase alone and in complex with 3′-dATP. Science 289 (2000) 1346-1349
-
(2000)
Science
, vol.289
, pp. 1346-1349
-
-
Bard, J.1
Zhelkovsky, A.M.2
Helmling, S.3
Earnest, T.N.4
Moore, C.L.5
Bohm, A.6
-
5
-
-
0035903113
-
Terminal deoxynucleotidyl transferase indiscriminately incorporates ribonucleotides and deoxyribonucleotides
-
Boule J.B., Rougeon F., and Papanicolaou C. Terminal deoxynucleotidyl transferase indiscriminately incorporates ribonucleotides and deoxyribonucleotides. J. Biol. Chem. 276 (2001) 31388-31389
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 31388-31389
-
-
Boule, J.B.1
Rougeon, F.2
Papanicolaou, C.3
-
6
-
-
3543012707
-
Crystallography & NMR system: A new software suite for macromolecular structure determination
-
Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54 (1998) 905-921
-
(1998)
Acta Crystallogr. D Biol. Crystallogr.
, vol.54
, pp. 905-921
-
-
Brunger, A.T.1
Adams, P.D.2
Clore, G.M.3
DeLano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.S.7
Kuszewski, J.8
Nilges, M.9
Pannu, N.S.10
-
7
-
-
34248349170
-
Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases
-
Castro C., Smidansky E., Maksimchuk K.R., Arnold J.J., Korneeva V.S., Götte M., Konigsberg W., and Cameron C.E. Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases. Proc. Natl. Acad. Sci. USA 104 (2007) 4267-4272
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 4267-4272
-
-
Castro, C.1
Smidansky, E.2
Maksimchuk, K.R.3
Arnold, J.J.4
Korneeva, V.S.5
Götte, M.6
Konigsberg, W.7
Cameron, C.E.8
-
8
-
-
59649110607
-
Nucleic acid polymerases use a general acid for nucleotidyl transfer
-
Castro C., Smidansky E.D., Arnold J.J., Maksimchuk K.R., Moustafa I., Uchida A., Götte M., Konigsberg W., and Cameron C.E. Nucleic acid polymerases use a general acid for nucleotidyl transfer. Nat. Struct. Mol. Biol. 16 (2009) 212-218
-
(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
Götte, M.7
Konigsberg, W.8
Cameron, C.E.9
-
9
-
-
0028103275
-
The CCP4 suite: programs for protein crystallography
-
Collaborative Computational Project Number 4 (CCP4)
-
Collaborative Computational Project Number 4 (CCP4). The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50 (1994) 760-763
-
(1994)
Acta Crystallogr. D Biol. Crystallogr.
, vol.50
, pp. 760-763
-
-
-
10
-
-
0031041188
-
Interplay of two uridylate-specific RNA binding sites in the translocation of poly(A) polymerase from vaccinia virus
-
Deng L., and Gershon P.D. Interplay of two uridylate-specific RNA binding sites in the translocation of poly(A) polymerase from vaccinia virus. EMBO J. 16 (1997) 1103-1113
-
(1997)
EMBO J.
, vol.16
, pp. 1103-1113
-
-
Deng, L.1
Gershon, P.D.2
-
12
-
-
0033613910
-
A polyadenylylation-specific RNA-contact site on the surface of the bifunctional vaccinia virus RNA modifying protein VP39 that is distinct from the mRNA 5′ end-binding "cleft"
-
Deng L., Johnson L., Neveu J.M., Hardin S., Wang S.-M., Lane W.S., and Gershon P.D. A polyadenylylation-specific RNA-contact site on the surface of the bifunctional vaccinia virus RNA modifying protein VP39 that is distinct from the mRNA 5′ end-binding "cleft". J. Mol. Biol. 285 (1999) 1417-1427
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1417-1427
-
-
Deng, L.1
Johnson, L.2
Neveu, J.M.3
Hardin, S.4
Wang, S.-M.5
Lane, W.S.6
Gershon, P.D.7
-
13
-
-
77956930528
-
Poly(A) adding enzymes
-
Boyer P.D. (Ed), Academic Press Inc., New York
-
Edmonds M. Poly(A) adding enzymes. In: Boyer P.D. (Ed). The Enzymes (1982), Academic Press Inc., New York 217-224
-
(1982)
The Enzymes
, pp. 217-224
-
-
Edmonds, M.1
-
14
-
-
0025280060
-
Polyadenylate polymerases
-
Dahlberg J., and Abelson J. (Eds), Academic Press, Inc., New York
-
Edmonds M. Polyadenylate polymerases. In: Dahlberg J., and Abelson J. (Eds). Methods in Enzymology (1990), Academic Press, Inc., New York 161-170
-
(1990)
Methods in Enzymology
, pp. 161-170
-
-
Edmonds, M.1
-
15
-
-
0036364652
-
A history of poly A sequences: from formation to factors to function
-
Edmonds M. A history of poly A sequences: from formation to factors to function. Prog. Nucleic Acid Res. Mol. Biol. 71 (2002) 285-389
-
(2002)
Prog. Nucleic Acid Res. Mol. Biol.
, vol.71
, pp. 285-389
-
-
Edmonds, M.1
-
16
-
-
33746375404
-
Mechanism of DNA translocation in a replicative hexameric helicase
-
Enemark E.J., and Joshua-Tor L. Mechanism of DNA translocation in a replicative hexameric helicase. Nature 442 (2006) 270-275
-
(2006)
Nature
, vol.442
, pp. 270-275
-
-
Enemark, E.J.1
Joshua-Tor, L.2
-
17
-
-
0024522801
-
Structure and stability of mRNA synthesized by vaccinia virus-encoded bacteriophage T7 RNA polymerase in mammalian cells. Importance of the 5′ untranslated leader
-
Fuerst T.R., and Moss B. Structure and stability of mRNA synthesized by vaccinia virus-encoded bacteriophage T7 RNA polymerase in mammalian cells. Importance of the 5′ untranslated leader. J. Mol. Biol. 206 (1989) 333-348
-
(1989)
J. Mol. Biol.
, vol.206
, pp. 333-348
-
-
Fuerst, T.R.1
Moss, B.2
-
18
-
-
0026781188
-
Transition from rapid processive to slow non-processive polyadenylation by vaccinia virus poly(A) polymerase catalytic subunit is regulated by the net length of the poly(A) tail
-
Gershon P.D., and Moss B. Transition from rapid processive to slow non-processive polyadenylation by vaccinia virus poly(A) polymerase catalytic subunit is regulated by the net length of the poly(A) tail. Genes Dev. 6 (1992) 1575-1586
-
(1992)
Genes Dev.
, vol.6
, pp. 1575-1586
-
-
Gershon, P.D.1
Moss, B.2
-
19
-
-
0027391646
-
Stimulation of poly(A) tail elongation by the VP39 subunit of the vaccinia virus-encoded poly(A) polymerase
-
Gershon P.D., and Moss B. Stimulation of poly(A) tail elongation by the VP39 subunit of the vaccinia virus-encoded poly(A) polymerase. J. Biol. Chem. 268 (1993) 2203-2210
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 2203-2210
-
-
Gershon, P.D.1
Moss, B.2
-
20
-
-
0027372353
-
Uridylate-containing RNA sequences determine specificity for binding and polyadenylation by the catalytic subunit of vaccinia virus poly(A) polymerase
-
Gershon P.D., and Moss B. Uridylate-containing RNA sequences determine specificity for binding and polyadenylation by the catalytic subunit of vaccinia virus poly(A) polymerase. EMBO J. 12 (1993) 4705-4714
-
(1993)
EMBO J.
, vol.12
, pp. 4705-4714
-
-
Gershon, P.D.1
Moss, B.2
-
21
-
-
0025771504
-
Poly(A) polymerase and a dissociable polyadenylation stimulatory factor encoded by vaccinia virus
-
Gershon P.D., Ahn B.-Y., Garfield M., and Moss B. Poly(A) polymerase and a dissociable polyadenylation stimulatory factor encoded by vaccinia virus. Cell 66 (1991) 1269-1278
-
(1991)
Cell
, vol.66
, pp. 1269-1278
-
-
Gershon, P.D.1
Ahn, B.-Y.2
Garfield, M.3
Moss, B.4
-
22
-
-
0032486584
-
Evidence that the RNA methylation and poly(A) polymerase stimulatory activities of vaccinia virus protein VP39 do not impinge upon one another
-
Gershon P.D., Shi X., and Hodel A.E. Evidence that the RNA methylation and poly(A) polymerase stimulatory activities of vaccinia virus protein VP39 do not impinge upon one another. Virology 246 (1998) 253-265
-
(1998)
Virology
, vol.246
, pp. 253-265
-
-
Gershon, P.D.1
Shi, X.2
Hodel, A.E.3
-
23
-
-
0035312659
-
Recent advances in FRET: distance determination in protein-DNA complexes
-
Hillisch A., Lorenz M., and Diekmann S. Recent advances in FRET: distance determination in protein-DNA complexes. Curr. Opin. Struct. Biol. 11 (2001) 201-207
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 201-207
-
-
Hillisch, A.1
Lorenz, M.2
Diekmann, S.3
-
24
-
-
0033168555
-
RNA binding characteristics and overall topology of the vaccinia poly(A) polymerase-processivity factor complex
-
Johnson L., and Gershon P.D. RNA binding characteristics and overall topology of the vaccinia poly(A) polymerase-processivity factor complex. Nucleic Acids Res. 27 (1999) 2708-2721
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 2708-2721
-
-
Johnson, L.1
Gershon, P.D.2
-
25
-
-
1642381309
-
Molecular flexibility and discontinuous translocation of a non-templated polymerase
-
Johnson L., Liu S., and Gershon P.D. Molecular flexibility and discontinuous translocation of a non-templated polymerase. J. Mol. Biol. 337 (2004) 843-885
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 843-885
-
-
Johnson, L.1
Liu, S.2
Gershon, P.D.3
-
26
-
-
84889120137
-
Improved methods for building protein models in electron density maps and the location of errors in these models
-
Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47 (1991) 110-119
-
(1991)
Acta Crystallogr. A
, vol.47
, pp. 110-119
-
-
Jones, T.A.1
Zou, J.Y.2
Cowan, S.W.3
Kjeldgaard, M.4
-
27
-
-
33751212468
-
Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism
-
Kapanidis A.N., Margeat E., Ho S.O., Kortkhonjia E., Weiss S., and Ebright R.H. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314 (2006) 1144-1147
-
(2006)
Science
, vol.314
, pp. 1144-1147
-
-
Kapanidis, A.N.1
Margeat, E.2
Ho, S.O.3
Kortkhonjia, E.4
Weiss, S.5
Ebright, R.H.6
-
28
-
-
42449084129
-
Protein factors in pre-mRNA 3′-end processing
-
Mandel C.R., Bai Y., and Tong L. Protein factors in pre-mRNA 3′-end processing. Cell. Mol. Life Sci. 65 (2008) 109-122
-
(2008)
Cell. Mol. Life Sci.
, vol.65
, pp. 109-122
-
-
Mandel, C.R.1
Bai, Y.2
Tong, L.3
-
29
-
-
35548959608
-
RNA-specific ribonucleotidyl transferases
-
Martin G., and Keller W. RNA-specific ribonucleotidyl transferases. RNA 13 (2007) 1834-1849
-
(2007)
RNA
, vol.13
, pp. 1834-1849
-
-
Martin, G.1
Keller, W.2
-
30
-
-
0034664049
-
Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP
-
Martin G., Keller W., and Doublie S. Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP. EMBO J. 19 (2000) 4193-4203
-
(2000)
EMBO J.
, vol.19
, pp. 4193-4203
-
-
Martin, G.1
Keller, W.2
Doublie, S.3
-
31
-
-
0016681178
-
Characterization of a polyriboadenylate polymerase from vaccinia virions
-
Moss B., Rosenblum E.N., and Gershowitz A. Characterization of a polyriboadenylate polymerase from vaccinia virions. J. Biol. Chem. 250 (1975) 4722-4729
-
(1975)
J. Biol. Chem.
, vol.250
, pp. 4722-4729
-
-
Moss, B.1
Rosenblum, E.N.2
Gershowitz, A.3
-
32
-
-
33646164166
-
Crystal structures of the vaccinia virus polyadenylate polymerase heterodimer: Insights into ATP selectivity and processivity
-
Moure C.M., Bowman B.R., Gershon P.D., and Quiocho F.A. Crystal structures of the vaccinia virus polyadenylate polymerase heterodimer: Insights into ATP selectivity and processivity. Mol. Cell 33 (2006) 339-349
-
(2006)
Mol. Cell
, vol.33
, pp. 339-349
-
-
Moure, C.M.1
Bowman, B.R.2
Gershon, P.D.3
Quiocho, F.A.4
-
33
-
-
0034732989
-
Location of cyanine-3 on double-stranded DNA: importance for fluorescence resonance energy transfer studies
-
Norman D.G., Grainger R.J., Uhrin D., and Lilley D.M. Location of cyanine-3 on double-stranded DNA: importance for fluorescence resonance energy transfer studies. Biochemistry 39 (2000) 6317-6324
-
(2000)
Biochemistry
, vol.39
, pp. 6317-6324
-
-
Norman, D.G.1
Grainger, R.J.2
Uhrin, D.3
Lilley, D.M.4
-
34
-
-
0035986681
-
Path of an RNA ligand around the surface of the vaccinia VP39 subunit of its cognate VP39-VP55 protein heterodimer
-
Oguro A., Johnson L., and Gershon P.D. Path of an RNA ligand around the surface of the vaccinia VP39 subunit of its cognate VP39-VP55 protein heterodimer. Chem. Biol. 9 (2002) 679-690
-
(2002)
Chem. Biol.
, vol.9
, pp. 679-690
-
-
Oguro, A.1
Johnson, L.2
Gershon, P.D.3
-
35
-
-
0031059866
-
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
-
36
-
-
33745823112
-
Mechanisms of helicases
-
Patel S.S., and Donmez I. Mechanisms of helicases. J. Biol. Chem. 281 (2006) 18265-18268
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 18265-18268
-
-
Patel, S.S.1
Donmez, I.2
-
37
-
-
33751218319
-
Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching
-
Revyakin A., Liu C., Ebright R.H., and Strick T.R. Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314 (2006) 1139-1143
-
(2006)
Science
, vol.314
, pp. 1139-1143
-
-
Revyakin, A.1
Liu, C.2
Ebright, R.H.3
Strick, T.R.4
-
38
-
-
0030865928
-
The surface region of the bifunctional vaccinia RNA modifying protein VP39 that interfaces with poly(A) polymerase is remote from the RNA binding cleft used for its mRNA 5′ cap methylation function
-
Shi X., Bernhardt T.G., Wang S.-M., and Gershon P.D. The surface region of the bifunctional vaccinia RNA modifying protein VP39 that interfaces with poly(A) polymerase is remote from the RNA binding cleft used for its mRNA 5′ cap methylation function. J. Biol. Chem. 272 (1997) 23292-23302
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 23292-23302
-
-
Shi, X.1
Bernhardt, T.G.2
Wang, S.-M.3
Gershon, P.D.4
-
39
-
-
0023918860
-
Vaccinia virus poly(A) polymerase: Specificity for nucleotides and nucleotide analogs
-
Shuman S., and Moss B. Vaccinia virus poly(A) polymerase: Specificity for nucleotides and nucleotide analogs. J. Biol. Chem. 263 (1988) 8405-8412
-
(1988)
J. Biol. Chem.
, vol.263
, pp. 8405-8412
-
-
Shuman, S.1
Moss, B.2
-
40
-
-
0032518374
-
A mechanism for all polymerases
-
Steitz T. A mechanism for all polymerases. Nature 391 (1998) 231-232
-
(1998)
Nature
, vol.391
, pp. 231-232
-
-
Steitz, T.1
-
41
-
-
34547097537
-
Saltatory forward movement of a poly(A) polymerase during poly(A) tail addition
-
Yoshizawa J.M., Li C., and Gershon P.D. Saltatory forward movement of a poly(A) polymerase during poly(A) tail addition. J. Biol. Chem. 282 (2007) 19144-19151
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 19144-19151
-
-
Yoshizawa, J.M.1
Li, C.2
Gershon, P.D.3
-
42
-
-
0033059981
-
Formation of mRNA 3′ ends in eukaryotes: Mechanism, regulation, and interrelationships with other steps in mRNA synthesis
-
Zhao J., Hyman L., and Moore C. Formation of mRNA 3′ ends in eukaryotes: Mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev. 63 (1999) 405-445
-
(1999)
Microbiol. Mol. Biol. Rev.
, vol.63
, pp. 405-445
-
-
Zhao, J.1
Hyman, L.2
Moore, C.3
|