-
1
-
-
0032530719
-
A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA
-
Allen, M.D., Yamasaki, K., Ohme-Takagi, M., Tateno, M., and Suzuki, M. (1998). A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. EMBO J. 17, 5484-5496.
-
(1998)
EMBO J.
, vol.17
, pp. 5484-5496
-
-
Allen, M.D.1
Yamasaki, K.2
Ohme-Takagi, M.3
Tateno, M.4
Suzuki, M.5
-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (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
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
5
-
-
0028385745
-
The 5′-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression
-
Baker, S.S., Wilhelm, K.S., and Thomashow, M.F. (1994). The 5′-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression. Plant Mol. Biol. 24, 701-713.
-
(1994)
Plant Mol. Biol.
, vol.24
, pp. 701-713
-
-
Baker, S.S.1
Wilhelm, K.S.2
Thomashow, M.F.3
-
6
-
-
9144257886
-
The Pfam protein families database
-
Bateman, A., et al. (2004). The Pfam protein families database. Nucleic Acids Res. 32, D138-141.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Bateman, A.1
-
7
-
-
0031004536
-
Arabidopsis thaliana ethylene-responsive element binding protein (AtEBP), an ethylene-inducible, GCC box DNA-binding protein interacts with an ocs element binding protein
-
Buttner, M., and Singh, K.B. (1997). Arabidopsis thaliana ethylene-responsive element binding protein (AtEBP), an ethylene-inducible, GCC box DNA-binding protein interacts with an ocs element binding protein. Proc. Natl. Acad. Sci. USA 94, 5961-5966.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 5961-5966
-
-
Buttner, M.1
Singh, K.B.2
-
8
-
-
0035883706
-
Homing endonucleases: Structural and functional insight into the catalysts of intron/intein mobility
-
Chevalier, B.S., and Stoddard, B.L. (2001). Homing endonucleases: Structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res. 29, 3757-3774.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 3757-3774
-
-
Chevalier, B.S.1
Stoddard, B.L.2
-
9
-
-
0031849661
-
Site-specific DNA binding using a variation of the double stranded RNA binding motif
-
Connolly, K.M., Wojciak, J.M., and Clubb, R.T. (1998). Site-specific DNA binding using a variation of the double stranded RNA binding motif. Nat. Struct. Biol. 5, 546-550.
-
(1998)
Nat. Struct. Biol.
, vol.5
, pp. 546-550
-
-
Connolly, K.M.1
Wojciak, J.M.2
Clubb, R.T.3
-
10
-
-
0030729344
-
Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family
-
Dalgaard, J.Z., Klar, A.J., Moser, M.J., Holley, W.R., Chatterjee, A., and Mian, I.S. (1997). Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. Nucleic Acids Res. 25, 4626-4638.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 4626-4638
-
-
Dalgaard, J.Z.1
Klar, A.J.2
Moser, M.J.3
Holley, W.R.4
Chatterjee, A.5
Mian, I.S.6
-
11
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar, R.C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
12
-
-
0034031131
-
Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression
-
Fujimoto, S.Y., Ohta, M., Usui, A., Shinshi, H., and Ohme-Takagi, M. (2000). Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell 12, 393-404.
-
(2000)
Plant Cell
, vol.12
, pp. 393-404
-
-
Fujimoto, S.Y.1
Ohta, M.2
Usui, A.3
Shinshi, H.4
Ohme-Takagi, M.5
-
13
-
-
0034656221
-
Invasion of a multitude of genetic niches by mobile endonuclease genes
-
Gimble, F.S. (2000). Invasion of a multitude of genetic niches by mobile endonuclease genes. FEMS Microbiol. Lett. 185, 99-107.
-
(2000)
FEMS Microbiol. Lett.
, vol.185
, pp. 99-107
-
-
Gimble, F.S.1
-
14
-
-
0032500520
-
Unique mode of GCC box recognition by the DNA-binding domain of ethylene-responsive element-binding factor (ERF domain) in plant
-
Hao, D., Ohme-Takagi, M., and Sarai, A. (1998). Unique mode of GCC box recognition by the DNA-binding domain of ethylene-responsive element-binding factor (ERF domain) in plant. J. Biol. Chem. 273, 26857-26861.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 26857-26861
-
-
Hao, D.1
Ohme-Takagi, M.2
Sarai, A.3
-
15
-
-
0037006987
-
Determinants in the sequence specific binding of two plant transcription factors, CBF1 and NtERF2, to the DRE and GCC motifs
-
Hao, D., Yamasaki, K., Sarai, A., and Ohme-Takagi, M. (2002). Determinants in the sequence specific binding of two plant transcription factors, CBF1 and NtERF2, to the DRE and GCC motifs. Biochemistry 41, 4202-4208.
-
(2002)
Biochemistry
, vol.41
, pp. 4202-4208
-
-
Hao, D.1
Yamasaki, K.2
Sarai, A.3
Ohme-Takagi, M.4
-
16
-
-
0030087776
-
Requirement of a CCGAC cis-acting element for cold induction of the BN115 gene from winter Brassica napus
-
Jiang, C., Iu, B., and Singh, J. (1996). Requirement of a CCGAC cis-acting element for cold induction of the BN115 gene from winter Brassica napus. Plant Mol. Biol. 30, 679-684.
-
(1996)
Plant Mol. Biol.
, vol.30
, pp. 679-684
-
-
Jiang, C.1
Iu, B.2
Singh, J.3
-
17
-
-
0033556230
-
RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants
-
Kagaya, Y., Ohmiya, K., and Hattori, T. (1999). RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res. 27, 470-478.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 470-478
-
-
Kagaya, Y.1
Ohmiya, K.2
Hattori, T.3
-
18
-
-
0031301752
-
Predicting protein structure using hidden Markov models
-
Karplus, K., Sjolander, K., Barrett, C., Cline, M., Haussler, D., Hughey, R., Holm, L., and Sander, C. (1997). Predicting protein structure using hidden Markov models. Proteins 1 (suppl.), 134-139.
-
(1997)
Proteins
, vol.1
, Issue.SUPPL.
, pp. 134-139
-
-
Karplus, K.1
Sjolander, K.2
Barrett, C.3
Cline, M.4
Haussler, D.5
Hughey, R.6
Holm, L.7
Sander, C.8
-
19
-
-
0034595501
-
Enhanced genome annotation using structural profiles in the program 3D-PSSM
-
Kelley, L.A., MacCallum, R.M., and Sternberg, M.J. (2000). Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299, 499-520.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 499-520
-
-
Kelley, L.A.1
MacCallum, R.M.2
Sternberg, M.J.3
-
20
-
-
0036184347
-
Adaptation for horizontal transfer in a homing endonuclease
-
Koufopanou, V., Goddard, M.R., and Burt, A. (2002). Adaptation for horizontal transfer in a homing endonuclease. Mol. Biol. Evol. 19, 239-246.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 239-246
-
-
Koufopanou, V.1
Goddard, M.R.2
Burt, A.3
-
21
-
-
0037389957
-
AINTEGUMENTA utilizes a mode of DNA recognition distinct from that used by proteins containing a single AP2 domain
-
Krizek, B.A. (2003). AINTEGUMENTA utilizes a mode of DNA recognition distinct from that used by proteins containing a single AP2 domain. Nucleic Acids Res. 31, 1859-1868.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 1859-1868
-
-
Krizek, B.A.1
-
22
-
-
0036086410
-
Recent improvements to the SMART domain-based sequence annotation resource
-
Letunic, I., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P., and Bork, P. (2002). Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30, 242-244.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 242-244
-
-
Letunic, I.1
Goodstadt, L.2
Dickens, N.J.3
Doerks, T.4
Schultz, J.5
Mott, R.6
Ciccarelli, F.7
Copley, R.R.8
Ponting, C.P.9
Bork, P.10
-
23
-
-
0037252683
-
CDD: A curated Entrez database of conserved domain alignments
-
Marchler-Bauer, A., et al. (2003). CDD: A curated Entrez database of conserved domain alignments. Nucleic Acids Res. 31, 383-387.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 383-387
-
-
Marchler-Bauer, A.1
-
24
-
-
11144354393
-
Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D
-
Matsuzaki, M., et al. (2004). Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428, 653-657.
-
(2004)
Nature
, vol.428
, pp. 653-657
-
-
Matsuzaki, M.1
-
25
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. (1995). SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
26
-
-
0034327422
-
DNA binding properties of the Arabidopsis floral development protein AINTEGUMENTA
-
Nole-Wilson, S., and Krizek, B.A. (2000). DNA binding properties of the Arabidopsis floral development protein AINTEGUMENTA. Nucleic Acids Res. 28, 4076-4082.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 4076-4082
-
-
Nole-Wilson, S.1
Krizek, B.A.2
-
27
-
-
0033486062
-
Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional represser MBD1
-
Ohki, I., Shimotake, N., Fujita, N., Nakao, M., and Shirakawa, M. (1999). Solution structure of the methyl-CpG-binding domain of the methylation- dependent transcriptional represser MBD1. EMBO J. 18, 6653-6661.
-
(1999)
EMBO J.
, vol.18
, pp. 6653-6661
-
-
Ohki, I.1
Shimotake, N.2
Fujita, N.3
Nakao, M.4
Shirakawa, M.5
-
28
-
-
0029240488
-
Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element
-
Ohme-Takagi, M., and Shinshi, H. (1995). Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7, 173-182.
-
(1995)
Plant Cell
, vol.7
, pp. 173-182
-
-
Ohme-Takagi, M.1
Shinshi, H.2
-
29
-
-
0032509105
-
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
-
Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T., and Chothia, C. (1998). Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol. 284, 1201-1210.
-
(1998)
J. Mol. Biol.
, vol.284
, pp. 1201-1210
-
-
Park, J.1
Karplus, K.2
Barrett, C.3
Hughey, R.4
Haussler, D.5
Hubbard, T.6
Chothia, C.7
-
30
-
-
0035024584
-
Overexpression of the tobacco Tsi1 gene encoding an EREBP/AP2-type transcription factor enhances resistance against pathogen attack and osmotic stress in tobacco
-
Park, J.M., Park, C.J., Lee, S.B., Ham, B.K., Shin, R., and Paek, K.H. (2001). Overexpression of the tobacco Tsi1 gene encoding an EREBP/AP2-type transcription factor enhances resistance against pathogen attack and osmotic stress in tobacco. Plant Cell 13, 1035-1046.
-
(2001)
Plant Cell
, vol.13
, pp. 1035-1046
-
-
Park, J.M.1
Park, C.J.2
Lee, S.B.3
Ham, B.K.4
Shin, R.5
Paek, K.H.6
-
31
-
-
0031845074
-
The AP2/EREBP family of plant transcription factors
-
Riechmann, J.L., and Meyerowitz, E.M. (1998). The AP2/EREBP family of plant transcription factors. Biol. Chem. 379, 633-646.
-
(1998)
Biol. Chem.
, vol.379
, pp. 633-646
-
-
Riechmann, J.L.1
Meyerowitz, E.M.2
-
32
-
-
0036290601
-
DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression
-
Sakuma, Y., Liu, Q., Dubouzet, J.G., Abe, H., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2002). DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression. Biochem. Biophys. Res. Commun. 290, 998-1009.
-
(2002)
Biochem. Biophys. Res. Commun.
, vol.290
, pp. 998-1009
-
-
Sakuma, Y.1
Liu, Q.2
Dubouzet, J.G.3
Abe, H.4
Shinozaki, K.5
Yamaguchi-Shinozaki, K.6
-
33
-
-
0028151655
-
Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns
-
Shub, D.A., Goodrich-Blair, H., and Eddy, S.R. (1994). Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. Trends Biochem. Sci. 19, 402-404.
-
(1994)
Trends Biochem. Sci.
, vol.19
, pp. 402-404
-
-
Shub, D.A.1
Goodrich-Blair, H.2
Eddy, S.R.3
-
34
-
-
0642367806
-
New types of conserved sequence domains in DNA-binding regions of homing endonucleases
-
Sitbon, E., and Pietrokovski, S. (2003). New types of conserved sequence domains in DNA-binding regions of homing endonucleases. Trends Biochem. Sci. 28, 473-477.
-
(2003)
Trends Biochem. Sci.
, vol.28
, pp. 473-477
-
-
Sitbon, E.1
Pietrokovski, S.2
-
35
-
-
0037047129
-
Selective interaction of plant homeodomain proteins mediates high DNA-binding affinity
-
Smith, H.M., Boschke, I., and Hake, S. (2002). Selective interaction of plant homeodomain proteins mediates high DNA-binding affinity. Proc. Natl. Acad. Sci. USA 99, 9579-9584.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 9579-9584
-
-
Smith, H.M.1
Boschke, I.2
Hake, S.3
-
36
-
-
0031017671
-
Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit
-
Stockinger, E.J., Gilmour, S.J., and Thomashow, M.F. (1997). Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc. Natl. Acad. Sci. USA 94, 1035-1040.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 1035-1040
-
-
Stockinger, E.J.1
Gilmour, S.J.2
Thomashow, M.F.3
-
37
-
-
0033498862
-
Plant cold acclimation: Freezing tolerance genes and regulatory mechanisms
-
Thomashow, M.F. (1999). Plant cold acclimation: Freezing tolerance genes and regulatory mechanisms. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50, 571-599.
-
(1999)
Annu. Rev. Plant Physiol. Plant Mol. Biol.
, vol.50
, pp. 571-599
-
-
Thomashow, M.F.1
-
38
-
-
0034931983
-
Two APETALA2-like genes of Picea abies are differentially expressed during development
-
Vahala, T., Oxelman, B., and von Arnold, S. (2001). Two APETALA2-like genes of Picea abies are differentially expressed during development. J. Exp. Bot. 52, 1111-1115.
-
(2001)
J. Exp. Bot.
, vol.52
, pp. 1111-1115
-
-
Vahala, T.1
Oxelman, B.2
Von Arnold, S.3
-
39
-
-
0037133558
-
Arm-site binding by lambda-integrase: Solution structure and functional characterization of its amino-terminal domain
-
Wojciak, J.M., Sarkar, D., Landy, A., and Clubb, R.T. (2002). Arm-site binding by lambda-integrase: Solution structure and functional characterization of its amino-terminal domain. Proc. Natl. Acad. Sci. USA 99, 3434-3439.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 3434-3439
-
-
Wojciak, J.M.1
Sarkar, D.2
Landy, A.3
Clubb, R.T.4
-
40
-
-
0036606136
-
A novel family of mobile genetic elements is limited to the germline genome in Tetrahymena thermophila
-
Wuitschick, J.D., Gershan, J.A., Lochowicz, A.J., Li, S., and Karrer, K.M. (2002). A novel family of mobile genetic elements is limited to the germline genome in Tetrahymena thermophila. Nucleic Acids Res. 30, 2524-2537.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 2524-2537
-
-
Wuitschick, J.D.1
Gershan, J.A.2
Lochowicz, A.J.3
Li, S.4
Karrer, K.M.5
-
41
-
-
0028370581
-
A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress
-
Yamaguchi-Shinozaki, K., and Shinozaki, K. (1994). A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6, 251-264.
-
(1994)
Plant Cell
, vol.6
, pp. 251-264
-
-
Yamaguchi-Shinozaki, K.1
Shinozaki, K.2
-
42
-
-
0030973457
-
The Pto kinase conferring resistance to tomato bacterial speck disease interacts with proteins that bind a cis-element of pathogenesis-related genes
-
Zhou, J., Tang, X., and Martin, G.B. (1997). The Pto kinase conferring resistance to tomato bacterial speck disease interacts with proteins that bind a cis-element of pathogenesis-related genes. EMBO J. 16, 3207-3218.
-
(1997)
EMBO J.
, vol.16
, pp. 3207-3218
-
-
Zhou, J.1
Tang, X.2
Martin, G.B.3
|