Shun-ichi Sekine | Laboratory for Transcription Structural Biology
Publications
Sekine S, Ehara H, Kujirai T, et al.
Structural perspectives on transcription in chromatin
Trends in Cell Biology
Thu Aug 17 00:00:00 JST 2023
doi: 10.1016/j.tcb.2023.07.011
Osawa T, Aoki M, Ehara H, et al.
Structures of dengue virus RNA replicase complexes
Molecular Cell
Wed Jul 12 00:00:00 JST 2023
doi: 10.1016/j.molcel.2023.06.023
Osumi K, Kujirai T, Ehara H, et al.
Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome
Journal of Molecular Biology
435(13), 168130 Sat Jul 01 00:00:00 JST 2023
doi: 10.1016/j.jmb.2023.168130
Kujirai T, Ehara H, Sekine S, Kurumizaka H.
Structural Transition of the Nucleosome during Transcription Elongation
Cells
12(10), 1388 Sun May 14 00:00:00 JST 2023
doi: 10.3390/cells12101388
Ohtomo H, Ito S, McKenzie N.J., et al.
H2A Ubiquitination Alters H3-tail Dynamics on Linker-DNA to Enhance H3K27 Methylation
Journal of Molecular Biology
435(4), 167936 Tue Feb 28 00:00:00 JST 2023
doi: 10.1016/j.jmb.2022.167936
Murayama Y, Ehara H, Aoki M, et al.
Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus
Science Advances
9(6), eade7093 Fri Feb 10 00:00:00 JST 2023
doi: 10.1126/sciadv.ade7093
Hirano R, Ehara H, Kujirai T, et al.
Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1
Nature Communications
13, 7287 Sat Nov 26 00:00:00 JST 2022
doi: 10.1038/s41467-022-35003-z
Inouye S, Sato J, Sahara-Miura Y, et al..
Reverse mutants of the catalytic 19 kDa mutant protein (nanoKAZ/nanoLuc) from Oplophorus luciferase with coelenterazine as preferred substrate
PLOS One
Wed Sep 21 00:00:00 JST 2022
doi: 10.1371/journal.pone.0272992
Ehara H, Kujirai T, et al.
Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT
Science
377(6611), abp9466 Thu Aug 18 00:00:00 JST 2022
doi: 10.1126/science.abp9466
Fukushima Y, Hatazawa S, Hirai S, et al.
Structural and biochemical analyses of the nucleosome containing Komagataella pastoris histones
J Biochem
172(2), 79-88 Fri Apr 29 00:00:00 JST 2022
doi: 10.1093/jb/mvac043
Hosaka T, Nomura T, Kubo M, et al.
Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers
PNAS
119(9), e2117433119 Wed Feb 23 00:00:00 JST 2022
doi: 10.1073/pnas.2117433119
Sekine S, Uejima T, Ehara H.
RNA Polymerase-associated Transcription Elongation Factors
RNA Polymerases as Molecular Motors
2nd ed, Chapter 4 Wed Dec 15 00:00:00 JST 2021
doi: 10.1039/9781839160561-00072
Ehara H, Kujirai T, et al.
Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Science
363(6428), 744-747 Sun Dec 01 00:00:00 JST 2019
doi: 10.1126/science.aav8912
Shimizu H, Saito A, Mikuni J, et al.
Discovery of a small molecule inhibitor targeting dengue virus NS5 RNA-dependent RNA polymerase.
Plos Neglected Tropical Diseases
13(11), e0007894 Fri Nov 01 00:00:00 JST 2019
doi: 10.1371/journal.pntd.0007894
Kujirai T, Ehara H, et al.
Structural basis of the nucleosome transition during RNA polymerase II passage.
Science
362(6414), 595-598 Sat Dec 01 00:00:00 JST 2018
doi: 10.1126/science.aau9904
Shimizu H, Tosaki A, Ohsawa N, et al.
Parallel homodimer structures of the extracellular domains of the voltage-gated sodium channel β4 subunit explain its role in cell-cell adhesion.
J. Biol. Chem.
292, 13428-13440 Fri Dec 01 00:00:00 JST 2017
Ooi WY, Murayama Y, Mekler V, et al.
A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation.
Nucleic Acids Research
46(1), 431-441 Fri Dec 01 00:00:00 JST 2017
doi: 10.1093/nar/gkx1162
Ehara H, Yokoyama T, Shigematsu H, et al.
Structure of the complete elongation complex of RNA polymerase II with basal factors.
Science
357(6354), 921-924 Wed Nov 01 00:00:00 JST 2017
doi: 10.1126/science.aan8552
Ehara H, Umehara T, Sekine SI, Yokoyama S.
Crystal structure of RNA polymerase II from Komagataella pastoris.
Biochemical and Biophysical Research Communications
487(2), 230-235 Sat May 27 00:00:00 JST 2017
doi: 10.1016/j.bbrc.2017.04.039
Tomabechi Y, Hosoya T, Ehara H, et al.
Crystal structure of nanoKAZ: The mutated 19 kDa component of Oplophorus luciferase catalyzing the bioluminescent reaction with coelenterazine.
Biochem. Biophys. Res. Commun.
470, 88-93 Thu Dec 01 00:00:00 JST 2016
Shimizu H, Miyazaki H, Ohsawa N, et al.
Structure-based site-directed photo-crosslinking analyses of multimeric cell-adhesive interactions of voltage-gated sodium channel β subunits.
Scientific Reports
6, 26618 Thu Dec 01 00:00:00 JST 2016
doi: 10.1038/srep26618
Ehara H, Makino M, Kodama K, et al.
Crystal structure of okadaic acid binding protein 2.1: a sponge protein implicated in cytotoxin accumulation.
Chembiochem
16, 1435-1439 Tue Dec 01 00:00:00 JST 2015
Antonopoulos IH, Murayama Y, Warner BA, et al.
Time-resolved Raman and polyacrylamide gel electrophoresis observations of nucleotide incorporation and misincorporation in RNA within a bacterial RNA polymerase crystal.
Biochemistry
54, 652-665 Tue Dec 01 00:00:00 JST 2015
Yanagisawa T, Ishii R, Hikida Y, et al.
A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA Cys.
J. Struct. Funct. Genomics.
16, 25-41 Tue Dec 01 00:00:00 JST 2015
Ito T, Masuda I, Yoshida K, et al.
Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Proc. Natl. Acad. Sci. U.S.A.
112, E4197-205 Tue Dec 01 00:00:00 JST 2015
Itoh Y, Sekine S, Yokoyama S.
Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB.
Nucleic Acids Res.
43, 9028-9038 Tue Dec 01 00:00:00 JST 2015
Sekine S, Murayama Y, Svetlov V, et al.
Ratcheting of RNA polymerase toward structural principles of RNA polymerase operations.
Transcription
6(3), 56-60 Tue Dec 01 00:00:00 JST 2015
doi: 10.1080/21541264.2015.1059922
Sekine S, Murayama Y, Svetlov V, et al.
The ratcheted and ratchetable structural states of RNA polymerase underlie multiple transcriptional functions.
Molecular Cell
57(3), 408-421 Sun Nov 01 00:00:00 JST 2015
doi: 10.1016/j.molcel.2014.12.014
Itoh Y, Bröcker MJ, Sekine S, et al.
Dimer-dimer interaction of the bacterial selenocysteine synthase SelA promotes functional active-site formation and catalytic specificity.
J. Mol. Biol.
426, 1723-1735 Mon Dec 01 00:00:00 JST 2014
Severinov K, Minakhin L, Sekine S, et al.
Molecular basis of RNA polymerase promoter specificity switch revealed through studies of Thermus bacteriophage transcription regulator.
Bacteriophage
4, e29399 Mon Dec 01 00:00:00 JST 2014
Higo T, Suka N, Ehara H, et al.
Development of a hexahistidine-3×FLAG-tandem affinity purification method for endogenous protein complexes in Pichia pastoris.
J. Struct. Funct. Genomics.
15, 191-199 Mon Dec 01 00:00:00 JST 2014
Naganuma M, Sekine S, Chong YE, et al.
The selective tRNA aminoacylation mechanism based on a single G•U pair.
Nature
510(7506), 507-511 Mon Dec 01 00:00:00 JST 2014
doi: 10.1038/nature13440
Tagami S, Sekine S, Minakhin L, et al.
Structural basis for promoter specificity switching of RNA polymerase by a phage factor.
Genes & Development
28(5), 521-531 Sat Nov 01 00:00:00 JST 2014
doi: 10.1101/gad.233916.113
Nakagawa H, Kuratani M, Goto-Ito S, et al.
Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA.
Proteins
81, 1232-1244 Sun Dec 01 00:00:00 JST 2013
Itoh Y, Bröcker MJ, Sekine S, et al.
The decameric SelA tRNA Sec ring structure reveals the mechanism of bacterial selenocysteine formation.
Science
340, 75-78 Sun Dec 01 00:00:00 JST 2013
Itoh Y, Sekine S, Suetsugu S, Yokoyama S.
Tertiary structure of bacterial selenocysteine tRNA.
Nucleic Acids Res.
41, 6729-6738 Sun Dec 01 00:00:00 JST 2013
Itoh Y, Brocker MJ, Sekine S, et al.
Decameric SelA•tRNASec Ring Structure Reveals Mechanism of Bacterial Selenocysteine Formation.
Science
340(6128), 75-78 Sun Dec 01 00:00:00 JST 2013
doi: 10.1126/science.1229521
Murayama Y, Sekine S, Yokoyama S.
Crystallization and preliminary X-ray crystallographic analyses of Thermus thermophilus backtracked RNA polymerase.
Acta Crystallographica. Section F
69, 174-177 Fri Feb 01 00:00:00 JST 2013
doi: 10.1107/S1744309113000055
Itoh Y, Sekine S, Yokoyama S.
Crystallization and preliminary X-ray crystallographic analysis of bacterial tRNA Sec in complex with seryl-tRNA synthetase.
Acta Crystallogr.
F68, 678-682 Sat Dec 01 00:00:00 JST 2012
Itoh Y, Sekine S, Yokoyama S.
Crystallization and preliminary X-ray crystallographic analysis of Aquifex aeolicus SelA, a bacterial selenocysteine synthase.
Acta Crystallogr.
F68, 1128-1133 Sat Dec 01 00:00:00 JST 2012
Sekine S, Tagami S, Yokoyama S.
Structural basis of transcription by bacterial and eukaryotic RNA polymerases.
Curr. Opin. Struct. Biol.
22, 110-118 Sat Dec 01 00:00:00 JST 2012
Hanawa-Suetsugu K, Kukimoto-Niino M, Mishima-Tsumagari C, et al.
Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms.
Proc. Natl. Acad. Sci. U. S. A.
109, 3305-3310 Sat Dec 01 00:00:00 JST 2012
Ehara H, Sekine S, Yokoyama S.
Crystal structure of the C17/25 subcomplex from Schizosaccharomyces pombe RNA Polymerase III.
Protein Sci.
20, 1558-1565 Thu Dec 01 00:00:00 JST 2011
Tagami S, Sekine S, Yokoyama S.
A novel conformation of RNA polymerase sheds light on the mechanism of transcription.
Transcription
2, 162-167 Thu Dec 01 00:00:00 JST 2011
Tagami S, Sekine S, Kumarevel T, et al.
Crystallization and preliminary X-ray crystallographic analysis of Thermus thermophilus transcription elongation complex bound to Gfh1.
Acta Crystallogr.
F66, 64-68 Wed Dec 01 00:00:00 JST 2010
Hikida Y, Kuratani M, Bessho Y, et al.
Crystal structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5- methyltransferase.
Acta Crystallogr.
D66, 1301-1307 Wed Dec 01 00:00:00 JST 2010
Kuratani M, Hirano M, Goto-Ito S, et al.
Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin.
J. Mol. Biol.
401, 323-333 Wed Dec 01 00:00:00 JST 2010
Chiba S, Itoh Y, Sekine S, Yokoyama S.
Structural basis for the major role of O-phosphoseryl-tRNA kinase in the UGA-specific encoding of selenocysteine.
Mol. Cell
39, 410-420 Wed Dec 01 00:00:00 JST 2010
Tagami S, Sekine S, Kumarevel T, et al.
Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.
Nature
468(7326), 978-982 Wed Dec 01 00:00:00 JST 2010
doi: 10.1038/nature09573
Itoh Y*, Sekine S*, Matsumoto E, et al.
Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs.
J. Mol. Biol.
385, 1456-1469 Tue Dec 01 00:00:00 JST 2009
Naganuma M, Sekine S, Fukunaga R, Yokoyama S.
Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.
Proc. Natl. Acad. Sci. U.S.A.
106, 8489-8494 Tue Dec 01 00:00:00 JST 2009
Konno M, Sumida T, Uchikawa E, et al.
Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP).
FEBS J.
276, 4763-4779 Tue Dec 01 00:00:00 JST 2009
Itoh Y, Chiba S, Sekine S, Yokoyama S.
Crystal structure of human selenocysteine tRNA.
Nucleic Acids Res.
37, 6259-6268 Tue Dec 01 00:00:00 JST 2009
Matsumoto E*, Sekine S*, Akasaka R, et al.
Structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus.
Acta Crystallogr.
F64, 453-458 Mon Dec 01 00:00:00 JST 2008
Itoh Y, Sekine S, Kuroishi C, et al.
Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii.
RNA Biol.
5, 169-177 Mon Dec 01 00:00:00 JST 2008
Goto-Ito S, Ishii R, Ito T, et al.
Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis.
Acta Crystallogr.
D63, 1059-1068 Sat Dec 01 00:00:00 JST 2007
Hiyama TB, Zhao M, Kitago Y, et al.
Structural basis of CoA recognition by the Pyrococcus singledomain CoA-binding proteins.
J. Struct. Funct. Genomics
7, 119-129 Sat Dec 01 00:00:00 JST 2007
Bessho Y, Shibata R, Sekine S, et al.
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.
Proc. Natl. Acad. Sci. U.S.A.
104, 8293-8298 Sat Dec 01 00:00:00 JST 2007
Shinkai A*, Sekine S*, Urushibata A, et al.
The putative DNA-binding protein Sto12a from the thermoacidophilic archaeon Sulfolobus tokodai i contains intrachain and interchain disulfide bonds.
J. Mol. Biol.
372, 1293-1304 Sat Dec 01 00:00:00 JST 2007
Kuratani M, Sakai H, Takahashi M, et al.
Crystal structures of tyrosyl-tRNA synthetases from Archaea.
J. Mol. Biol.
355, 395-408 Fri Dec 01 00:00:00 JST 2006
Iwasaki W, Sekine S, Kuroishi C, et al.
Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase.
J. Mol. Biol.
360, 329-342 Fri Dec 01 00:00:00 JST 2006
Sasaki HM, Sekine S, Sengoku T, et al.
Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase.
Proc. Natl. Acad. Sci. U.S.A.
103, 14744-14749 Fri Dec 01 00:00:00 JST 2006
Sekine S, Shichiri M, Bernier S, et al.
Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase.
Structure
14, 1791-1799 Fri Dec 01 00:00:00 JST 2006
Kuratani M, Ishii R, Bessho Y, et al.
Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus.
J. Biol. Chem.
280, 16002-16008 Thu Dec 01 00:00:00 JST 2005
Artsimovitch I, Patlan V, Sekine S, et al.
Structural basis for transcription regulation by alarmone ppGpp.
Cell
117, 299-310 Wed Dec 01 00:00:00 JST 2004
Randau L, Schauer S, Ambrogelly A, et al.
tRNA recognition by glutamyl-tRNA reductase.
J. Biol. Chem.
279, 34931-34937 Wed Dec 01 00:00:00 JST 2004
Hanawa-Suetsugu K, Sekine S, Sakai H, et al.
Crystal structure of elongation factor P from Thermus thermophilus HB8.
Proc. Natl. Acad. Sci. U.S.A.
101, 9595-9600 Wed Dec 01 00:00:00 JST 2004
Vassylyeva MN, Sakai H, Matsuura T, et al.
Cloning, expression, purification, crystallization and initial crystallographic analysis of the lysinebiosynthesis LysX protein from Thermus thermophilus HB8.
Acta Crystallogr.
D59, 1651-1652 Mon Dec 01 00:00:00 JST 2003
Sekine S, Nureki O, Dubois DY, et al.
ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding.
EMBO J.
22, 676-688 Mon Dec 01 00:00:00 JST 2003
Fukai S, Nureki O, Sekine S, et al.
Mechanism of molecular interactions for tRNA Val recognition by valyl-tRNA synthetase.
RNA
9, 100-111 Mon Dec 01 00:00:00 JST 2003
Sakai H, Vassylyeva MN, Matsuura T, et al.
Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8.
J. Mol. Biol.
332, 729-740 Mon Dec 01 00:00:00 JST 2003
Vassylyeva MN, Lee J, Sekine S, et al.
Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus.
Acta Crystallogr.
D58, 1497-1500 Sun Dec 01 00:00:00 JST 2002
Vassylyev DG, Sekine S, Laptenko O, et al.
Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution.
Nature
417, 712-719 Sun Dec 01 00:00:00 JST 2002
Sekine S, Nureki O, Shimada A, et al.
Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase.
Nature Struct. Biol.
8, 203-206 Sat Dec 01 00:00:00 JST 2001
Sekine S, Shimada A, Nureki O, et al.
Crucial role of the HIGH-loop lysine for the catalytic activity of arginyltRNA synthetase.
J. Biol. Chem.
276, 3723-3726 Sat Dec 01 00:00:00 JST 2001
Fukai S, Nureki O, Sekine S, et al.
Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA Val and valyl-tRNA synthetase.
Cell
103, 793-803 Fri Dec 01 00:00:00 JST 2000
Sekine S, Nureki O, Tateno M, Yokoyama S.
The identity determinants required for the discrimination between tRNA Glu and tRNA Asp by glutamyl-tRNA synthetase from Escherichia coli.
Eur. J. Biochem.
261, 354-360 Wed Dec 01 00:00:00 JST 1999
Madore E, Florentz C, Giegé, et al.
Effect of modified nucleotides on Escherichia coli tRNA Glu structure and on its aminoacylation by glutamyl-tRNA synthetase. Predominant and distinct roles of the mnm 5 and s 2 modifications of U34.
Eur. J. Biochem.
266, 1128-1135 Wed Dec 01 00:00:00 JST 1999
Sekine S, Nureki O, Sakamoto K, et al.
Major identity determinants in the augmented D helix of tRNA Glu from Escherichia coli.
J. Mol. Biol.
256, 685-700 Sun Dec 01 00:00:00 JST 1996
Nureki O, Vassylyev DG, Katayanagi K, et al.
Architectures of class-defining and specific domains of glutamyl-tRNA synthetase.
Science
267, 1958-1965 Fri Dec 01 00:00:00 JST 1995
Tateno M, Nureki O, Sekine S, et al.
A threedimensional structure model of the complex of glutamyl-tRNA synthetase and its cognate tRNA.
FEBS Letters
377, 77-81 Fri Dec 01 00:00:00 JST 1995
* denotes equal contribution.