-
1
-
-
14244272868
-
PHENIX: Building new software for automated crystallographic structure determination
-
Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC. 2002. PHENIX: Building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58: 1948-1954.
-
(2002)
Acta Crystallogr D Biol Crystallogr
, vol.58
, pp. 1948-1954
-
-
Adams, P.D.1
Grosse-Kunstleve, R.W.2
Hung, L.W.3
Ioerger, T.R.4
McCoy, A.J.5
Moriarty, N.W.6
Read, R.J.7
Sacchettini, J.C.8
Sauter, N.K.9
Terwilliger, T.C.10
-
2
-
-
1242309517
-
Decoding the genome: A modified view
-
Agris PF. 2004. Decoding the genome: A modified view. Nucleic Acids Res 32: 223-238.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 223-238
-
-
Agris, P.F.1
-
4
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
5
-
-
33646806139
-
5C methyltransferase specific for 16 S rRNA nucleotide 1407
-
5C methyltransferase specific for 16 S rRNA nucleotide 1407. J Mol Biol 359: 777-786.
-
(2006)
J Mol Biol
, vol.359
, pp. 777-786
-
-
Andersen, N.M.1
Douthwaite, S.2
-
6
-
-
2442686628
-
A novel partial modification at C2501 in Escherichia coli 23S ribosomal RNA
-
DOI 10.1261/rna.5259404
-
Andersen TE, Porse BT, Kirpekar F. 2004. A novel partial modification at C2501 in Escherichia coli 23S ribosomal RNA. RNA 10: 907-913. (Pubitemid 38669763)
-
(2004)
RNA
, vol.10
, Issue.6
, pp. 907-913
-
-
Andersen, T.1
Porse, B.T.2
Kirpekar, F.3
-
7
-
-
0028103275
-
The CCP4 Suite: Programs for protein crystallography
-
Bailey S. 1994. The CCP4 Suite: Programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50: 760-763.
-
(1994)
Acta Crystallogr D Biol Crystallogr
, vol.50
, pp. 760-763
-
-
Bailey, S.1
-
8
-
-
0142147324
-
The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Ψ-synthase also acting on tRNAs
-
DOI 10.1261/rna.5520403
-
Behm-Ansmant I, Urban A, Ma X, Yu YT, Motorin Y, Branlant C. 2003. The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Ψ-synthase also acting on tRNAs. RNA 9: 1371-1382. (Pubitemid 37310868)
-
(2003)
RNA
, vol.9
, Issue.11
, pp. 1371-1382
-
-
Behm-Ansmant, I.1
Urban, A.2
Ma, X.3
Yu, Y.-T.4
Motorin, Y.5
Branlant, C.6
-
9
-
-
34748878464
-
The Saccharomyces cerevisiae Pus2 protein encoded by YGL063w ORF is a mitochondrial tRNA:Ψ27/28-synthase
-
DOI 10.1261/rna.605607
-
Behm-Ansmant I, Branlant C, Motorin Y. 2007. The Saccharomyces cerevisiae Pus2 protein encoded by YGL063w ORF is a mitochondrial tRNA:Ψ27/28- synthase. RNA 13: 1641-1647. (Pubitemid 47481672)
-
(2007)
RNA
, vol.13
, Issue.10
, pp. 1641-1647
-
-
Behm-Ansmant, I.1
Branlant, C.2
Motorin, Y.3
-
10
-
-
4344605018
-
Thermus thermophilus L11 methyltransferase, PrmA, is dispensable for growth and preferentially modifies free ribosomal protein L11 prior to ribosome assembly
-
DOI 10.1128/JB.186.17.5819-5825.2004
-
Cameron DM, Gregory ST, Thompson J, Suh MJ, Limbach PA, Dahlberg AE. 2004. Thermus thermophilus L11 methyltransferase, PrmA, is dispensable for growth and preferentially modifies free ribosomal protein L11 prior to ribosome assembly. J Bacteriol 186: 5819-5825. (Pubitemid 39128655)
-
(2004)
Journal of Bacteriology
, vol.186
, Issue.17
, pp. 5819-5825
-
-
Cameron, D.M.1
Gregory, S.T.2
Thompson, J.3
Suh, M.-J.4
Limbach, P.A.5
Dahlberg, A.E.6
-
12
-
-
33846468457
-
Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA
-
DOI 10.1038/sj.emboj.7601508, PII 7601508
-
Demirci H, Gregory ST, Dahlberg AE, Jogl G. 2007. Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA. EMBO J 26: 567-577. (Pubitemid 46160956)
-
(2007)
EMBO Journal
, vol.26
, Issue.2
, pp. 567-577
-
-
Demirci, H.1
Gregory, S.T.2
Dahlberg, A.E.3
Jogl, G.4
-
13
-
-
55549136068
-
Crystal structure of the Thermus thermophilus 16 S rRNA methyltransferase RsmC in complex with cofactor and substrate guanosine
-
Demirci H, Gregory ST, Dahlberg AE, Jogl G. 2008a. Crystal structure of the Thermus thermophilus 16 S rRNA methyltransferase RsmC in complex with cofactor and substrate guanosine. J Biol Chem 283: 26548-26556.
-
(2008)
J Biol Chem
, vol.283
, pp. 26548-26556
-
-
Demirci, H.1
Gregory, S.T.2
Dahlberg, A.E.3
Jogl, G.4
-
14
-
-
46049109106
-
Multiple-Site Trimethylation of Ribosomal Protein L11 by the PrmA Methyltransferase
-
DOI 10.1016/j.str.2008.03.016, PII S0969212608001810
-
Demirci H, Gregory ST, Dahlberg AE, Jogl G. 2008b. Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase. Structure 16: 1059-1066. (Pubitemid 351899284)
-
(2008)
Structure
, vol.16
, Issue.7
, pp. 1059-1066
-
-
Demirci, H.1
Gregory, S.T.2
Dahlberg, A.E.3
Jogl, G.4
-
15
-
-
64049099242
-
Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 59-methylthioadenosine
-
Demirci H, Belardinelli R, Seri E, Gregory ST, Gualerzi C, Dahlberg AE, Jogl G. 2009. Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 59-methylthioadenosine. J Mol Biol 388: 271-282.
-
(2009)
J Mol Biol
, vol.388
, pp. 271-282
-
-
Demirci, H.1
Belardinelli, R.2
Seri, E.3
Gregory, S.T.4
Gualerzi, C.5
Dahlberg, A.E.6
Jogl, G.7
-
16
-
-
34548722786
-
Identifying modifications in RNA by MALDI mass spectrometry
-
Douthwaite S, Kirpekar F. 2007. Identifying modifications in RNA by MALDI mass spectrometry. Methods Enzymol 425: 1-20.
-
(2007)
Methods Enzymol
, vol.425
, pp. 1-20
-
-
Douthwaite, S.1
Kirpekar, F.2
-
18
-
-
49649114605
-
Protein structure modeling with MODELLER
-
Eswar N, Eramian D, Webb B, Shen MY, Sali A. 2008. Protein structure modeling with MODELLER. Methods Mol Biol 426: 145-159.
-
(2008)
Methods Mol Biol
, vol.426
, pp. 145-159
-
-
Eswar, N.1
Eramian, D.2
Webb, B.3
Shen, M.Y.4
Sali, A.5
-
19
-
-
0345096517
-
5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate
-
5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate. Structure 11: 1609-1620.
-
(2003)
Structure
, vol.11
, pp. 1609-1620
-
-
Foster, P.G.1
Nunes, C.R.2
Greene, P.3
Moustakas, D.4
Stroud, R.M.5
-
20
-
-
70350602056
-
The structure of the ribosome with elongation factor G trapped in the post-translocational state
-
Gao YG, Selmer M, Dunham CM, Weixlbaumer A, Kelley AC, Ramakrishnan V. 2009. The structure of the ribosome with elongation factor G trapped in the post-translocational state. Science 326: 694-699.
-
(2009)
Science
, vol.326
, pp. 694-699
-
-
Gao, Y.G.1
Selmer, M.2
Dunham, C.M.3
Weixlbaumer, A.4
Kelley, A.C.5
Ramakrishnan, V.6
-
23
-
-
33645943707
-
Influence of phylogeny on posttranscriptional modification of rRNA in thermophilic prokaryotes: The complete modification map of 16S rRNA of Thermus thermophilus
-
Guymon R, Pomerantz SC, Crain PF, McCloskey JA. 2006. Influence of phylogeny on posttranscriptional modification of rRNA in thermophilic prokaryotes: The complete modification map of 16S rRNA of Thermus thermophilus. Biochemistry 45: 4888-4899.
-
(2006)
Biochemistry
, vol.45
, pp. 4888-4899
-
-
Guymon, R.1
Pomerantz, S.C.2
Crain, P.F.3
McCloskey, J.A.4
-
24
-
-
33646767729
-
5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain
-
5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain. J Mol Biol 360: 774-787.
-
(2006)
J Mol Biol
, vol.360
, pp. 774-787
-
-
Hallberg, B.M.1
Ericsson, U.B.2
Johnson, K.A.3
Andersen, N.M.4
Douthwaite, S.5
Nordlund, P.6
Beuscher IV, A.E.7
Erlandsen, H.8
-
25
-
-
0035850879
-
Disruption of Thermus thermophilus genes by homologous recombination using a thermostable kanamycin-resistant marker
-
DOI 10.1016/S0014-5793(01)02926-X, PII S001457930102926X
-
Hashimoto Y, Yano T, Kuramitsua S, Kagamiyama H. 2001. Disruption of Thermus thermophilus genes by homologous recombination using a thermostable kanamycin-resistant marker. FEBS Lett 506: 231-234. (Pubitemid 32964819)
-
(2001)
FEBS Letters
, vol.506
, Issue.3
, pp. 231-234
-
-
Hashimoto, Y.1
Yano, T.2
Kuramitsu, S.3
Kagamiyama, H.4
-
26
-
-
0015494418
-
Mechanism of kasugamycin resistance in Escherichia coli
-
Helser TL, Davies JE, Dahlberg JE. 1972. Mechanism of kasugamycin resistance in Escherichia coli. Nat New Biol 235: 6-9.
-
(1972)
Nat New Biol
, vol.235
, pp. 6-9
-
-
Helser, T.L.1
Davies, J.E.2
Dahlberg, J.E.3
-
27
-
-
0025262173
-
Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): A vehicle for direct determination of three-dimensional structure
-
Hendrickson WA, Horton JR, LeMaster DM. 1990. Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): A vehicle for direct determination of three-dimensional structure. EMBO J 9: 1665-1672.
-
(1990)
EMBO J
, vol.9
, pp. 1665-1672
-
-
Hendrickson, W.A.1
Horton, J.R.2
LeMaster, D.M.3
-
29
-
-
0032730861
-
Directed evolution of thermostable kanamycin-resistance gene: A convenient selection marker for Thermus thermophilus
-
Hoseki J, Yano T, Koyama Y, Kuramitsu S, Kagamiyama H. 1999. Directed evolution of thermostable kanamycin-resistance gene: A convenient selection marker for Thermus thermophilus. J Biochem 126: 951-956.
-
(1999)
J Biochem
, vol.126
, pp. 951-956
-
-
Hoseki, J.1
Yano, T.2
Koyama, Y.3
Kuramitsu, S.4
Kagamiyama, H.5
-
30
-
-
34247199024
-
How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA
-
Hur S, Stroud RM. 2007. How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA. Mol Cell 26: 189-203.
-
(2007)
Mol Cell
, vol.26
, pp. 189-203
-
-
Hur, S.1
Stroud, R.M.2
-
31
-
-
66449110287
-
DOCK 6: Combining techniques to model RNA-small molecule complexes
-
Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA, James TL, Kuntz ID. 2009. DOCK 6: Combining techniques to model RNA-small molecule complexes. RNA 15: 1219-1230.
-
(2009)
RNA
, vol.15
, pp. 1219-1230
-
-
Lang, P.T.1
Brozell, S.R.2
Mukherjee, S.3
Pettersen, E.F.4
Meng, E.C.5
Thomas, V.6
Rizzo, R.C.7
Case, D.A.8
James, T.L.9
Kuntz, I.D.10
-
32
-
-
50249136103
-
Automated macromolecular model building for X-ray crystallography using ARP/wARP
-
version 7
-
Langer G, Cohen SX, Lamzin VS, Perrakis A. 2008. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3: 1171-1179.
-
(2008)
Nat Protoc
, vol.3
, pp. 1171-1179
-
-
Langer, G.1
Cohen, S.X.2
Lamzin, V.S.3
Perrakis, A.4
-
34
-
-
14844293080
-
A unique RNA fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function
-
DOI 10.1016/j.cell.2004.12.037
-
Lee TT, Agarwalla S, Stroud RM. 2005. A unique RNA fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell 120: 599-611. (Pubitemid 40343073)
-
(2005)
Cell
, vol.120
, Issue.5
, pp. 599-611
-
-
Lee, T.T.1
Agarwalla, S.2
Stroud, R.M.3
-
35
-
-
0034682446
-
5C DNA methyl transferases use different cysteine residues as catalysts
-
5C DNA methyl transferases use different cysteine residues as catalysts. Proc Natl Acad Sci 97: 8263-8265.
-
(2000)
Proc Natl Acad Sci
, vol.97
, pp. 8263-8265
-
-
Liu, Y.1
Santi, D.V.2
-
36
-
-
0028841409
-
Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes
-
Malone T, Blumenthal RM, Cheng X. 1995. Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J Mol Biol 253: 618-632.
-
(1995)
J Mol Biol
, vol.253
, pp. 618-632
-
-
Malone, T.1
Blumenthal, R.M.2
Cheng, X.3
-
37
-
-
34447508216
-
Phaser crystallographic software
-
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. 2007. Phaser crystallographic software. J Appl Crystallogr 40: 658-674.
-
(2007)
J Appl Crystallogr
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
39
-
-
0032821744
-
5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: Identification of the gene and substrate specificity of the enzyme
-
5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: Identification of the gene and substrate specificity of the enzyme. RNA 5: 1105-1118.
-
(1999)
RNA
, vol.5
, pp. 1105-1118
-
-
Motorin, Y.1
Grosjean, H.2
-
40
-
-
0031870753
-
The yeast tRNA:pseudouridine synthase Pus1p displays a multisite substrate specificity
-
DOI 10.1017/S1355838298980396
-
Motorin Y, Keith G, Simon C, Foiret D, Simos G, Hurt E, Grosjean H. 1998. The yeast tRNA:pseudouridine synthase Pus1p displays a multisite substrate specificity. RNA 4: 856-869. (Pubitemid 28317833)
-
(1998)
RNA
, vol.4
, Issue.7
, pp. 856-869
-
-
Motorin, Y.1
Keith, G.2
Simon, C.3
Foiret, D.4
Simos, G.5
Hurt, E.6
Grosjean, H.7
-
42
-
-
2342650072
-
Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli
-
O'Farrell HC, Scarsdale JN, Rife JP. 2004. Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli. J Mol Biol 339: 337-353.
-
(2004)
J Mol Biol
, vol.339
, pp. 337-353
-
-
O'Farrell, H.C.1
Scarsdale, J.N.2
Rife, J.P.3
-
43
-
-
0037184536
-
Selection of tRNA by the ribosome requires a transition from an open to a closed form
-
Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V. 2002. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111: 721-732.
-
(2002)
Cell
, vol.111
, pp. 721-732
-
-
Ogle, J.M.1
Murphy, F.V.2
Tarry, M.J.3
Ramakrishnan, V.4
-
44
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
DOI 10.1016/S0076-6879(97)76066-X
-
Otwinowski Z, Minor W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307-326. (Pubitemid 27085611)
-
(1997)
Methods in Enzymology
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
45
-
-
34748912322
-
The PUA domain - A structural and functional overview
-
DOI 10.1111/j.1742-4658.2007.06031.x
-
Pérez-Arellano I, Gallego J, Cervera J. 2007. The PUA domain - a structural and functional overview. FEBS J 274: 4972-4984. (Pubitemid 47481183)
-
(2007)
FEBS Journal
, vol.274
, Issue.19
, pp. 4972-4984
-
-
Perez-Arellano, I.1
Gallego, J.2
Cervera, J.3
-
47
-
-
33749354360
-
Structure of the 70S ribosome complexed with mRNA and tRNA
-
Selmer M, Dunham CM, Murphy FV 4th, Weixlbaumer A, Petry S, Kelley AC, Weir JR, Ramakrishnan V. 2006. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313: 1935-1942.
-
(2006)
Science
, vol.313
, pp. 1935-1942
-
-
Selmer, M.1
Dunham, C.M.2
Murphy IV, F.V.3
Weixlbaumer, A.4
Petry, S.5
Kelley, A.C.6
Weir, J.R.7
Ramakrishnan, V.8
-
49
-
-
0034699518
-
Structure of the 30S ribosomal subunit
-
Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. 2000. Structure of the 30S ribosomal subunit. Nature 407: 327-339.
-
(2000)
Nature
, vol.407
, pp. 327-339
-
-
Wimberly, B.T.1
De Brodersen2
Clemons Jr., W.M.3
Morgan-Warren, R.J.4
Carter, A.P.5
Vonrhein, C.6
Hartsch, T.7
Ramakrishnan, V.8
|