| Year |
Citation |
Score |
| 2023 |
Kukimoto-Niino M, Ihara K, Mishima-Tsumagari C, Inoue M, Fukui Y, Yokoyama S, Shirouzu M. Structural basis for the dual GTPase specificity of the DOCK10 guanine nucleotide exchange factor. Biochemical and Biophysical Research Communications. 653: 12-20. PMID 36848820 DOI: 10.1016/j.bbrc.2023.02.054 |
0.339 |
|
| 2021 |
Murayama K, Kato-Murayama M, Sato T, Hosaka T, Ishiguro K, Mizuno T, Kitao K, Honma T, Yokoyama S, Tanaka Y, Shirouzu M. Anthocyanin 5,3'-aromatic acyltransferase from Gentiana triflora, a structural insight into biosynthesis of a blue anthocyanin. Phytochemistry. 186: 112727. PMID 33743393 DOI: 10.1016/j.phytochem.2021.112727 |
0.321 |
|
| 2018 |
Sengoku T, Suzuki T, Dohmae N, Watanabe C, Honma T, Hikida Y, Yamaguchi Y, Takahashi H, Yokoyama S, Yanagisawa T. Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP. Nature Chemical Biology. PMID 29440735 DOI: 10.1038/s41589-018-0002-y |
0.336 |
|
| 2018 |
Sridharan U, Kuramitsu S, Yokoyama S, Kumarevel T, Ponnuraj K. Crystal structure of Aquifex aeolicus gene product Aq1627: a putative phosphoglucosamine mutase reveals a unique C-terminal end-to-end disulfide linkage. Molecular Biosystems. 13: 1370-1376. PMID 28548163 DOI: 10.1039/c7mb00182g |
0.335 |
|
| 2017 |
Ehara H, Umehara T, Sekine SI, Yokoyama S. Crystal structure of RNA polymerase II from Komagataella pastoris. Biochemical and Biophysical Research Communications. 487: 230-235. PMID 28412353 DOI: 10.1016/j.bbrc.2017.04.039 |
0.301 |
|
| 2017 |
Goto-Ito S, Ito T, Yokoyama S. Trm5 and TrmD: Two Enzymes from Distinct Origins Catalyze the Identical tRNA Modification, m¹G37. Biomolecules. 7. PMID 28335556 DOI: 10.3390/biom7010032 |
0.315 |
|
| 2016 |
Thiruselvam V, Kumarevel T, Karthe P, Kuramitsu S, Yokoyama S, Ponnuswamy MN. Crystal structure analysis of a hypothetical protein (MJ0366) from Methanocaldococcus jannaschii revealed a novel topological arrangement of the knot fold. Biochemical and Biophysical Research Communications. 482: 264-269. PMID 27845039 DOI: 10.1016/j.bbrc.2016.11.052 |
0.352 |
|
| 2016 |
Watanabe Y, Yanai H, Kanagawa M, Suzuki S, Tamura S, Okada K, Baba S, Kumasaka T, Agari Y, Chen L, Fu ZQ, Chrzas J, Wang BC, Nakagawa N, Ebihara A, ... ... Yokoyama S, et al. Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii. Acta Crystallographica. Section F, Structural Biology Communications. 72: 627-35. PMID 27487927 DOI: 10.1107/S2053230X1600978X |
0.361 |
|
| 2015 |
Ito T, Masuda I, Yoshida K, Goto-Ito S, Sekine S, Suh SW, Hou YM, Yokoyama S. Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD. Proceedings of the National Academy of Sciences of the United States of America. 112: E4197-205. PMID 26183229 DOI: 10.1073/pnas.1422981112 |
0.317 |
|
| 2015 |
Ehara H, Makino M, Kodama K, Konoki K, Ito T, Sekine SI, Fukuzawa S, Yokoyama S, Tachibana K. Crystal Structure of Okadaic Acid Binding Protein 2.1: A Sponge Protein Implicated in Cytotoxin Accumulation. Chembiochem : a European Journal of Chemical Biology. PMID 25965326 DOI: 10.1002/cbic.201500141 |
0.327 |
|
| 2015 |
Yanagisawa T, Ishii R, Hikida Y, Fukunaga R, Sengoku T, Sekine S, Yokoyama S. A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.). Journal of Structural and Functional Genomics. 16: 25-41. PMID 25618148 DOI: 10.1007/S10969-015-9193-6 |
0.358 |
|
| 2014 |
Itoh Y, Bröcker MJ, Sekine S, Söll D, Yokoyama S. Dimer-dimer interaction of the bacterial selenocysteine synthase SelA promotes functional active-site formation and catalytic specificity. Journal of Molecular Biology. 426: 1723-35. PMID 24456689 DOI: 10.1016/J.Jmb.2014.01.003 |
0.368 |
|
| 2013 |
Sampei G, Kanagawa M, Baba S, Shimasaki T, Taka H, Mitsui S, Fujiwara S, Yanagida Y, Kusano M, Suzuki S, Terao K, Kawai H, Fukai Y, Nakagawa N, Ebihara A, ... ... Yokoyama S, et al. Structures and reaction mechanisms of the two related enzymes, PurN and PurU. Journal of Biochemistry. 154: 569-79. PMID 24108189 DOI: 10.1093/jb/mvt090 |
0.336 |
|
| 2013 |
Won EY, Xie Y, Takemoto C, Chen L, Liu ZJ, Wang BC, Lee D, Woo EJ, Park SG, Shirouzu M, Yokoyama S, Kim SJ, Chi SW. High-resolution crystal structure of the catalytic domain of human dual-specificity phosphatase 26. Acta Crystallographica. Section D, Biological Crystallography. 69: 1160-70. PMID 23695260 DOI: 10.1107/S0907444913004770 |
0.317 |
|
| 2013 |
Itoh Y, Bröcker MJ, Sekine S, Hammond G, Suetsugu S, Söll D, Yokoyama S. Decameric SelA•tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation. Science (New York, N.Y.). 340: 75-8. PMID 23559248 DOI: 10.1126/Science.1229521 |
0.41 |
|
| 2012 |
Yanagisawa T, Sumida T, Ishii R, Yokoyama S. A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site. Acta Crystallographica. Section D, Biological Crystallography. 69: 5-15. PMID 23275158 DOI: 10.1107/S0907444912039881 |
0.339 |
|
| 2012 |
Murayama K, Kato-Murayama M, Akasaka R, Terada T, Yokoyama S, Shirouzu M. Structure of the Rho-specific guanine nucleotide-exchange factor Xpln. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 68: 1455-9. PMID 23192023 DOI: 10.1107/S1744309112045265 |
0.303 |
|
| 2012 |
Kitamura A, Nishimoto M, Sengoku T, Shibata R, Jäger G, Björk GR, Grosjean H, Yokoyama S, Bessho Y. Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1). The Journal of Biological Chemistry. 287: 43950-60. PMID 23091054 DOI: 10.1074/jbc.M112.409300 |
0.312 |
|
| 2012 |
Kawahara-Kobayashi A, Masuda A, Araiso Y, Sakai Y, Kohda A, Uchiyama M, Asami S, Matsuda T, Ishitani R, Dohmae N, Yokoyama S, Kigawa T, Nureki O, Kiga D. Simplification of the genetic code: restricted diversity of genetically encoded amino acids. Nucleic Acids Research. 40: 10576-84. PMID 22909996 DOI: 10.1093/nar/gks786 |
0.391 |
|
| 2012 |
Murayama K, Kato-Murayama M, Hosaka T, Sotokawauchi A, Yokoyama S, Arima K, Shirouzu M. Crystal structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L. Journal of Molecular Biology. 423: 386-96. PMID 22841692 DOI: 10.1016/j.jmb.2012.07.013 |
0.377 |
|
| 2012 |
Hanawa-Suetsugu K, Kukimoto-Niino M, Mishima-Tsumagari C, Akasaka R, Ohsawa N, Sekine S, Ito T, Tochio N, Koshiba S, Kigawa T, Terada T, Shirouzu M, Nishikimi A, Uruno T, Katakai T, ... ... Yokoyama S, et al. Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms. Proceedings of the National Academy of Sciences of the United States of America. 109: 3305-10. PMID 22331897 DOI: 10.1073/pnas.1113512109 |
0.349 |
|
| 2012 |
Morishita EC, Murayama K, Kato-Murayama M, Ishizuka-Katsura Y, Tomabechi Y, Hayashi T, Terada T, Handa N, Shirouzu M, Akiyama T, Yokoyama S. Crystal structures of the armadillo repeat domain of adenomatous polyposis coli and its complex with the tyrosine-rich domain of Sam68. Structure (London, England : 1993). 19: 1496-508. PMID 22000517 DOI: 10.1016/j.str.2011.07.013 |
0.353 |
|
| 2011 |
Awai T, Ochi A, Sengoku T, Hirata A, Bessho Y, Yokoyama S, Hori H. Substrate tRNA recognition mechanism of a multisite-specific tRNA methyltransferase, Aquifex aeolicus Trm1, based on the X-ray crystal structure. The Journal of Biological Chemistry. 286: 35236-46. PMID 21844194 DOI: 10.1074/jbc.M111.253641 |
0.375 |
|
| 2011 |
Kitamura A, Sengoku T, Nishimoto M, Yokoyama S, Bessho Y. Crystal structure of the bifunctional tRNA modification enzyme MnmC from Escherichia coli. Protein Science : a Publication of the Protein Society. 20: 1105-13. PMID 21574198 DOI: 10.1002/pro.659 |
0.405 |
|
| 2011 |
Sato S, Mimasu S, Sato A, Hino N, Sakamoto K, Umehara T, Yokoyama S. Crystallographic study of a site-specifically cross-linked protein complex with a genetically incorporated photoreactive amino acid. Biochemistry. 50: 250-7. PMID 21128684 DOI: 10.1021/bi1016183 |
0.323 |
|
| 2010 |
Tagami S, Sekine S, Kumarevel T, Hino N, Murayama Y, Kamegamori S, Yamamoto M, Sakamoto K, Yokoyama S. Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein. Nature. 468: 978-82. PMID 21124318 DOI: 10.1038/nature09573 |
0.302 |
|
| 2010 |
Hikida Y, Kuratani M, Bessho Y, Sekine SI, Yokoyama S. Structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5-methyltransferase. Acta Crystallographica. Section D, Biological Crystallography. 66: 1301-7. PMID 21123870 DOI: 10.1107/S0907444910037558 |
0.34 |
|
| 2010 |
Tanaka T, Niwa H, Yutani K, Kuramitsu S, Yokoyama S, Kumarevel T. Crystal structure of TTHA0061, an uncharacterized protein from Thermus thermophilus HB8, reveals a novel fold. Biochemical and Biophysical Research Communications. 400: 258-64. PMID 20728427 DOI: 10.1016/j.bbrc.2010.08.054 |
0.329 |
|
| 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. Molecular Cell. 39: 410-20. PMID 20705242 DOI: 10.1016/j.molcel.2010.07.018 |
0.333 |
|
| 2010 |
Ito T, Kiyasu N, Matsunaga R, Takahashi S, Yokoyama S. Structure of nondiscriminating glutamyl-tRNA synthetase from Thermotoga maritima. Acta Crystallographica. Section D, Biological Crystallography. 66: 813-20. PMID 20606262 DOI: 10.1107/S0907444910019086 |
0.312 |
|
| 2010 |
Shida M, Arakawa A, Ishii R, Kishishita S, Takagi T, Kukimoto-Niino M, Sugano S, Tanaka A, Shirouzu M, Yokoyama S. Direct inter-subdomain interactions switch between the closed and open forms of the Hsp70 nucleotide-binding domain in the nucleotide-free state. Acta Crystallographica. Section D, Biological Crystallography. 66: 223-32. PMID 20179333 DOI: 10.1107/S0907444909053979 |
0.329 |
|
| 2010 |
Jeyakanthan J, Drevland RM, Gayathri DR, Velmurugan D, Shinkai A, Kuramitsu S, Yokoyama S, Graham DE. Substrate specificity determinants of the methanogen homoaconitase enzyme: structure and function of the small subunit. Biochemistry. 49: 2687-96. PMID 20170198 DOI: 10.1021/Bi901766Z |
0.304 |
|
| 2009 |
Jeyakanthan J, Takada K, Sawano M, Ogasahara K, Mizutani H, Kunishima N, Yokoyama S, Yutani K. Crystal Structural and Functional Analysis of the Putative Dipeptidase from Pyrococcus horikoshii OT3. Journal of Biophysics (Hindawi Publishing Corporation : Online). 2009: 434038. PMID 20130794 DOI: 10.1155/2009/434038 |
0.303 |
|
| 2009 |
Padmanabhan B, Bessho Y, Ebihara A, Antonyuk SV, Ellis MJ, Strange RW, Kuramitsu S, Watanabe N, Hasnain SS, Yokoyama S. Structure of putative 4-amino-4-deoxychorismate lyase from Thermus thermophilus HB8 Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 65: 1234-1239. PMID 20054118 DOI: 10.1107/S1744309109050052 |
0.404 |
|
| 2009 |
Strange RW, Antonyuk SV, Ellis MJ, Bessho Y, Kuramitsu S, Shinkai A, Yokoyama S, Hasnain SS. Structure of a putative beta-phosphoglucomutase (TM1254) from Thermotoga maritima. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 65: 1218-21. PMID 20054115 DOI: 10.1107/S1744309109046302 |
0.308 |
|
| 2009 |
Antonyuk SV, Strange RW, Ellis MJ, Bessho Y, Kuramitsu S, Inoue Y, Yokoyama S, Hasnain SS. Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate). Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 65: 1209-13. PMID 20054113 DOI: 10.1107/S1744309109044935 |
0.343 |
|
| 2009 |
Antonyuk SV, Ellis MJ, Strange RW, Bessho Y, Kuramitsu S, Shinkai A, Yokoyama S, Hasnain SS. Structure of SurE protein from Aquifex aeolicus VF5 at 1.5 A resolution. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 65: 1204-8. PMID 20054112 DOI: 10.1107/S1744309109043814 |
0.302 |
|
| 2009 |
Jeyakanthan J, Thamotharan S, Velmurugan D, Rao VS, Nagarajan S, Shinkai A, Kuramitsu S, Yokoyama S. New structural insights and molecular-modelling studies of 4-methyl-5-beta-hydroxyethylthiazole kinase from Pyrococcus horikoshii OT3 (PhThiK). Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 65: 978-86. PMID 19851002 DOI: 10.1107/S1744309109036033 |
0.302 |
|
| 2009 |
Kumarevel T, Tanaka T, Bessho Y, Shinkai A, Yokoyama S. Crystal structure of hydrogenase maturating endopeptidase HycI from Escherichia coli. Biochemical and Biophysical Research Communications. 389: 310-4. PMID 19720045 DOI: 10.1016/j.bbrc.2009.08.135 |
0.359 |
|
| 2009 |
He F, Saito K, Kobayashi N, Harada T, Watanabe S, Kigawa T, Güntert P, Ohara O, Tanaka A, Unzai S, Muto Y, Yokoyama S. Structural and functional characterization of the NHR1 domain of the Drosophila neuralized E3 ligase in the notch signaling pathway. Journal of Molecular Biology. 393: 478-95. PMID 19683535 DOI: 10.1016/j.jmb.2009.08.020 |
0.304 |
|
| 2009 |
Naganuma M, Sekine S, Fukunaga R, Yokoyama S. Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization. Proceedings of the National Academy of Sciences of the United States of America. 106: 8489-94. PMID 19423669 DOI: 10.1073/Pnas.0901572106 |
0.34 |
|
| 2009 |
Sakamoto K, Murayama K, Oki K, Iraha F, Kato-Murayama M, Takahashi M, Ohtake K, Kobayashi T, Kuramitsu S, Shirouzu M, Yokoyama S. Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography. Structure (London, England : 1993). 17: 335-44. PMID 19278648 DOI: 10.1016/j.str.2009.01.008 |
0.329 |
|
| 2009 |
He F, Dang W, Abe C, Tsuda K, Inoue M, Watanabe S, Kobayashi N, Kigawa T, Matsuda T, Yabuki T, Aoki M, Seki E, Harada T, Tomabechi Y, Terada T, ... ... Yokoyama S, et al. Solution structure of the RNA binding domain in the human muscleblind-like protein 2. Protein Science : a Publication of the Protein Society. 18: 80-91. PMID 19177353 DOI: 10.1002/pro.17 |
0.327 |
|
| 2008 |
Sarai N, Kagawa W, Fujikawa N, Saito K, Hikiba J, Tanaka K, Miyagawa K, Kurumizaka H, Yokoyama S. Biochemical analysis of the N-terminal domain of human RAD54B. Nucleic Acids Research. 36: 5441-50. PMID 18718930 DOI: 10.1093/nar/gkn516 |
0.317 |
|
| 2008 |
Ragunathan P, Kumarevel T, Agari Y, Shinkai A, Kuramitsu S, Yokoyama S, Ponnuraj K. Crystal structure of ST2348, a CBS domain protein, from hyperthermophilic archaeon Sulfolobus tokodaii. Biochemical and Biophysical Research Communications. 375: 124-8. PMID 18691556 DOI: 10.1016/j.bbrc.2008.07.140 |
0.355 |
|
| 2008 |
Kumarevel T, Nakano N, Ponnuraj K, Gopinath SC, Sakamoto K, Shinkai A, Kumar PK, Yokoyama S. Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector L-glutamine: implications of effector binding in molecular association and DNA binding. Nucleic Acids Research. 36: 4808-20. PMID 18653535 DOI: 10.1093/nar/gkn456 |
0.303 |
|
| 2008 |
Ohnishi S, Tochio N, Tomizawa T, Akasaka R, Harada T, Seki E, Sato M, Watanabe S, Fujikura Y, Koshiba S, Terada T, Shirouzu M, Tanaka A, Kigawa T, Yokoyama S. Structural basis for controlling the dimerization and stability of the WW domains of an atypical subfamily. Protein Science : a Publication of the Protein Society. 17: 1531-41. PMID 18562638 DOI: 10.1110/ps.035329.108 |
0.324 |
|
| 2008 |
Matsumoto E, Sekine SI, Akasaka R, Otta Y, Katsura K, Inoue M, Kaminishi T, Terada T, Shirouzu M, Yokoyama S. Structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 64: 453-8. PMID 18540050 DOI: 10.1107/S1744309108012074 |
0.337 |
|
| 2008 |
Ishitani R, Yokoyama S, Nureki O. Structure, dynamics, and function of RNA modification enzymes. Current Opinion in Structural Biology. 18: 330-9. PMID 18539024 DOI: 10.1016/j.sbi.2008.05.003 |
0.488 |
|
| 2008 |
Kishishita S, Shimizu K, Murayama K, Terada T, Shirouzu M, Yokoyama S, Kunishima N. Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2. Acta Crystallographica. Section D, Biological Crystallography. 64: 397-406. PMID 18391406 DOI: 10.1107/S0907444908000723 |
0.333 |
|
| 2008 |
Nishimura M, Kaminishi T, Takemoto C, Kawazoe M, Yoshida T, Tanaka A, Sugano S, Shirouzu M, Ohkubo T, Yokoyama S, Kobayashi Y. Crystal structure of human ribosomal protein L10 core domain reveals eukaryote-specific motifs in addition to the conserved fold. Journal of Molecular Biology. 377: 421-30. PMID 18258260 DOI: 10.1016/j.jmb.2008.01.003 |
0.342 |
|
| 2007 |
Nishimura M, Kaminishi T, Kawazoe M, Shirouzu M, Takemoto C, Yokoyama S, Tanaka A, Sugano S, Yoshida T, Ohkubo T, Kobayashi Y. Purification, crystallization and preliminary X-ray diffraction study of human ribosomal protein L10 core domain. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 63: 950-2. PMID 18007048 DOI: 10.1107/S1744309107048142 |
0.33 |
|
| 2007 |
Kumarevel T, Tanaka T, Nishio M, Gopinath SC, Takio K, Shinkai A, Kumar PK, Yokoyama S. Crystal structure of the MarR family regulatory protein, ST1710, from Sulfolobus tokodaii strain 7. Journal of Structural Biology. 161: 9-17. PMID 17933554 DOI: 10.1016/j.jsb.2007.08.017 |
0.307 |
|
| 2007 |
Shinkai A, Sekine S, Urushibata A, Terada T, Shirouzu M, Yokoyama S. The putative DNA-binding protein Sto12a from the thermoacidophilic archaeon Sulfolobus tokodaii contains intrachain and interchain disulfide bonds. Journal of Molecular Biology. 372: 1293-304. PMID 17720190 DOI: 10.1016/j.jmb.2007.07.051 |
0.34 |
|
| 2007 |
Ishii R, Minagawa A, Takaku H, Takagi M, Nashimoto M, Yokoyama S. The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 63: 637-41. PMID 17671357 DOI: 10.1107/S1744309107033623 |
0.35 |
|
| 2007 |
He F, Umehara T, Tsuda K, Inoue M, Kigawa T, Matsuda T, Yabuki T, Aoki M, Seki E, Terada T, Shirouzu M, Tanaka A, Sugano S, Muto Y, Yokoyama S. Solution structure of the zinc finger HIT domain in protein FON. Protein Science : a Publication of the Protein Society. 16: 1577-87. PMID 17656577 DOI: 10.1110/ps.062635107 |
0.317 |
|
| 2007 |
Suzuki S, Tatsuguchi A, Matsumoto E, Kawazoe M, Kaminishi T, Shirouzu M, Muto Y, Takemoto C, Yokoyama S. Structural characterization of the ribosome maturation protein, RimM Journal of Bacteriology. 189: 6397-6406. PMID 17616598 DOI: 10.1128/JB.00024-07 |
0.325 |
|
| 2007 |
Doi-Katayama Y, Hayashi F, Inoue M, Yabuki T, Aoki M, Seki E, Matsuda T, Kigawa T, Yoshida M, Shirouzu M, Terada T, Hayashizaki Y, Yokoyama S, Hirota H. Solution structure of the general transcription factor 2I domain in mouse TFII-I protein. Protein Science : a Publication of the Protein Society. 16: 1788-92. PMID 17600150 DOI: 10.1110/ps.072792007 |
0.317 |
|
| 2007 |
Nakamura Y, Umehara T, Tanaka A, Horikoshi M, Padmanabhan B, Yokoyama S. Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome Biochemical and Biophysical Research Communications. 359: 503-509. PMID 17555716 DOI: 10.1016/j.bbrc.2007.05.138 |
0.323 |
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| 2007 |
Fukunaga R, Yokoyama S. Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus. Journal of Molecular Biology. 370: 128-41. PMID 17512006 DOI: 10.1016/J.Jmb.2007.04.050 |
0.391 |
|
| 2007 |
Bessho Y, Shibata R, Sekine S, Murayama K, Higashijima K, Hori-Takemoto C, Shirouzu M, Kuramitsu S, Yokoyama S. Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Proceedings of the National Academy of Sciences of the United States of America. 104: 8293-8. PMID 17488812 DOI: 10.1073/pnas.0700402104 |
0.37 |
|
| 2007 |
Fukunaga R, Yokoyama S. Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea. Nature Structural & Molecular Biology. 14: 272-9. PMID 17351629 DOI: 10.1038/Nsmb1219 |
0.319 |
|
| 2007 |
Fukunaga R, Yokoyama S. Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii. Acta Crystallographica. Section D, Biological Crystallography. 63: 390-400. PMID 17327676 DOI: 10.1107/S090744490605640X |
0.335 |
|
| 2007 |
Yoshikawa S, Arai R, Kinoshita Y, Uchikubo-Kamo T, Wakamatsu T, Akasaka R, Masui R, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S. Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate. Acta Crystallographica. Section D, Biological Crystallography. 63: 357-65. PMID 17327673 DOI: 10.1107/S0907444906055442 |
0.358 |
|
| 2007 |
Shibata R, Bessho Y, Shinkai A, Nishimoto M, Fusatomi E, Terada T, Shirouzu M, Yokoyama S. Crystal structure and RNA-binding analysis of the archaeal transcription factor NusA. Biochemical and Biophysical Research Communications. 355: 122-8. PMID 17288993 DOI: 10.1016/j.bbrc.2007.01.119 |
0.306 |
|
| 2007 |
Kondo N, Nakagawa N, Ebihara A, Chen L, Liu ZJ, Wang BC, Yokoyama S, Kuramitsu S, Masui R. Structure of dNTP-inducible dNTP triphosphohydrolase: insight into broad specificity for dNTPs and triphosphohydrolase-type hydrolysis. Acta Crystallographica. Section D, Biological Crystallography. 63: 230-9. PMID 17242516 DOI: 10.1107/S0907444906049262 |
0.386 |
|
| 2007 |
Dong X, Kato-Murayama M, Muramatsu T, Mori H, Shirouzu M, Bessho Y, Yokoyama S. The crystal structure of leucyl/phenylalanyl-tRNA-protein transferase from Escherichia coli. Protein Science : a Publication of the Protein Society. 16: 528-34. PMID 17242373 DOI: 10.1110/ps.062616107 |
0.312 |
|
| 2007 |
Nakamura Y, Umehara T, Nakano K, Jang MK, Shirouzu M, Morita S, Uda-Tochio H, Hamana H, Terada T, Adachi N, Matsumoto T, Tanaka A, Horikoshi M, Ozato K, Padmanabhan B, ... Yokoyama S, et al. Crystal structure of the human BRD2 bromodomain: insights into dimerization and recognition of acetylated histone H4. The Journal of Biological Chemistry. 282: 4193-201. PMID 17148447 DOI: 10.1074/Jbc.M605971200 |
0.32 |
|
| 2006 |
Hiyama TB, Zhao M, Kitago Y, Yao M, Sekine S, Terada T, Kuroishi C, Liu ZJ, Rose JP, Kuramitsu S, Shirouzu M, Watanabe N, Yokoyama S, Tanaka I, Wang BC. Structural basis of CoA recognition by the Pyrococcus single-domain CoA-binding proteins. Journal of Structural and Functional Genomics. 7: 119-29. PMID 17342453 DOI: 10.1007/S10969-007-9015-6 |
0.35 |
|
| 2006 |
Murayama K, Shirouzu M, Kawasaki Y, Kato-Murayama M, Hanawa-Suetsugu K, Sakamoto A, Katsura Y, Suenaga A, Toyama M, Terada T, Taiji M, Akiyama T, Yokoyama S. Crystal structure of the rac activator, Asef, reveals its autoinhibitory mechanism. The Journal of Biological Chemistry. 282: 4238-4242. PMID 17190834 DOI: 10.1074/jbc.C600234200 |
0.301 |
|
| 2006 |
Dong X, Bessho Y, Shibata R, Nishimoto M, Shirouzu M, Kuramitsu S, Yokoyama S. Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8. Rna Biology. 3: 115-22. PMID 17114947 |
0.373 |
|
| 2006 |
Yanagisawa T, Ishii R, Fukunaga R, Nureki O, Yokoyama S. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of pyrrolysyl-tRNA synthetase from the methanogenic archaeon Methanosarcina mazei. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 62: 1031-3. PMID 17012805 DOI: 10.1107/S1744309106036700 |
0.54 |
|
| 2006 |
Sasaki HM, Sekine S, Sengoku T, Fukunaga R, Hattori M, Utsunomiya Y, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S. Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase. Proceedings of the National Academy of Sciences of the United States of America. 103: 14744-9. PMID 17003130 DOI: 10.1073/Pnas.0603182103 |
0.679 |
|
| 2006 |
Handa N, Kukimoto-Niino M, Akasaka R, Kishishita S, Murayama K, Terada T, Inoue M, Kigawa T, Kose S, Imamoto N, Tanaka A, Hayashizaki Y, Shirouzu M, Yokoyama S. The crystal structure of mouse Nup35 reveals atypical RNP motifs and novel homodimerization of the RRM domain. Journal of Molecular Biology. 363: 114-24. PMID 16962612 DOI: 10.1016/j.jmb.2006.07.089 |
0.335 |
|
| 2006 |
Nakano N, Okazaki N, Satoh S, Takio K, Kuramitsu S, Shinkai A, Yokoyama S. Structure of the stand-alone RAM-domain protein from Thermus thermophilus HB8. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 62: 855-60. PMID 16946463 DOI: 10.1107/S1744309106031150 |
0.378 |
|
| 2006 |
Inagaki E, Ohshima N, Takahashi H, Kuroishi C, Yokoyama S, Tahirov TH. Crystal structure of Thermus thermophilus Delta1-pyrroline-5-carboxylate dehydrogenase. Journal of Molecular Biology. 362: 490-501. PMID 16934832 DOI: 10.1016/j.jmb.2006.07.048 |
0.301 |
|
| 2006 |
Kukimoto-Niino M, Takagi T, Akasaka R, Murayama K, Uchikubo-Kamo T, Terada T, Inoue M, Watanabe S, Tanaka A, Hayashizaki Y, Kigawa T, Shirouzu M, Yokoyama S. Crystal structure of the RUN domain of the RAP2-interacting protein x. The Journal of Biological Chemistry. 281: 31843-53. PMID 16928684 DOI: 10.1074/jbc.M604960200 |
0.34 |
|
| 2006 |
Iwasaki W, Sekine S, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S. Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase. Journal of Molecular Biology. 360: 329-42. PMID 16753178 DOI: 10.1016/j.jmb.2006.04.068 |
0.323 |
|
| 2006 |
Hattori M, Mizohata E, Tatsuguchi A, Shibata R, Kishishita S, Murayama K, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S. Crystal structure of the single-domain rhodanese homologue TTHA0613 from Thermus thermophilus HB8. Proteins. 64: 284-7. PMID 16680676 DOI: 10.1002/prot.20937 |
0.675 |
|
| 2006 |
Ebihara A, Yao M, Masui R, Tanaka I, Yokoyama S, Kuramitsu S. Crystal structure of hypothetical protein TTHB 192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain Protein Science. 15: 1494-1499. PMID 16672237 DOI: 10.1110/ps.062131106 |
0.345 |
|
| 2006 |
Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell. 125: 287-300. PMID 16630817 DOI: 10.1016/j.cell.2006.01.054 |
0.521 |
|
| 2006 |
Hamada T, Ito Y, Abe T, Hayashi F, Güntert P, Inoue M, Kigawa T, Terada T, Shirouzu M, Yoshida M, Tanaka A, Sugano S, Yokoyama S, Hirota H. Solution structure of the antifreeze-like domain of human sialic acid synthase. Protein Science : a Publication of the Protein Society. 15: 1010-6. PMID 16597820 DOI: 10.1110/ps.051700406 |
0.349 |
|
| 2006 |
Arai R, Yoshikawa S, Murayama K, Imai Y, Takahashi R, Shirouzu M, Yokoyama S. Structure of human ubiquitin-conjugating enzyme E2 G2 (UBE2G2/UBC7). Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 62: 330-4. PMID 16582478 DOI: 10.1107/S1744309106009006 |
0.35 |
|
| 2006 |
Hondoh T, Kato A, Yokoyama S, Kuroda Y. Computer-aided NMR assay for detecting natively folded structural domains. Protein Science : a Publication of the Protein Society. 15: 871-83. PMID 16522794 DOI: 10.1110/ps.051880406 |
0.309 |
|
| 2006 |
Kuratani M, Sakai H, Takahashi M, Yanagisawa T, Kobayashi T, Murayama K, Chen L, Liu ZJ, Wang BC, Kuroishi C, Kuramitsu S, Terada T, Bessho Y, Shirouzu M, Sekine S, ... Yokoyama S, et al. Crystal structures of tyrosyl-tRNA synthetases from Archaea. Journal of Molecular Biology. 355: 395-408. PMID 16325203 DOI: 10.1016/J.Jmb.2005.10.073 |
0.338 |
|
| 2006 |
Hattori M, Mizohata E, Manzoku M, Bessho Y, Murayama K, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S. Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8. Proteins. 61: 1117-20. PMID 16250002 DOI: 10.1002/prot.20692 |
0.664 |
|
| 2006 |
Kishishita S, Tatsuguchi A, Ushikoshi-Nakayama R, Terada T, Kuramitsu S, Park SY, Tame JR, Shirouzu M, Yokoyama S. Crystal structure of a conserved hypothetical protein TT1751 from Thermus thermophilus HB8. Proteins. 57: 883-7. PMID 15481054 DOI: 10.1002/prot.20282 |
0.328 |
|
| 2005 |
Pioszak AA, Murayama K, Nakagawa N, Ebihara A, Kuramitsu S, Shirouzu M, Yokoyama S. Structures of a putative RNA 5-methyluridine methyltransferase, Thermus thermophilus TTHA1280, and its complex with S-adenosyl-L-homocysteine. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 61: 867-74. PMID 16511182 DOI: 10.1107/S1744309105029842 |
0.424 |
|
| 2005 |
Fukunaga R, Ishitani R, Nureki O, Yokoyama S. Crystallization of leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Pyrococcus horikoshii. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 61: 30-2. PMID 16508082 DOI: 10.1107/S1744309104021827 |
0.508 |
|
| 2005 |
Murayama K, Kato-Murayama M, Katsura K, Uchikubo-Kamo T, Yamaguchi-Hirafuji M, Kawazoe M, Akasaka R, Hanawa-Suetsugu K, Hori-Takemoto C, Terada T, Shirouzu M, Yokoyama S. Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 Å resolution Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 61: 26-29. PMID 16508081 DOI: 10.1107/S1744309104032555 |
0.316 |
|
| 2005 |
Mizohata E, Sakai H, Fusatomi E, Terada T, Murayama K, Shirouzu M, Yokoyama S. Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon Aeropyrum pernix K1. Journal of Molecular Biology. 354: 317-29. PMID 16214169 DOI: 10.1016/j.jmb.2005.09.006 |
0.371 |
|
| 2005 |
Fukunaga R, Yokoyama S. Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator-base recognition. Nature Structural & Molecular Biology. 12: 915-22. PMID 16155584 DOI: 10.1038/Nsmb985 |
0.345 |
|
| 2005 |
Tukalo M, Yaremchuk A, Fukunaga R, Yokoyama S, Cusack S. The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation. Nature Structural & Molecular Biology. 12: 923-30. PMID 16155583 DOI: 10.1038/Nsmb986 |
0.356 |
|
| 2005 |
Lokanath NK, Ohshima N, Takio K, Shiromizu I, Kuroishi C, Okazaki N, Kuramitsu S, Yokoyama S, Miyano M, Kunishima N. Crystal structure of novel NADP-dependent 3-hydroxyisobutyrate dehydrogenase from Thermus thermophilus HB8. Journal of Molecular Biology. 352: 905-17. PMID 16126223 DOI: 10.1016/j.jmb.2005.07.068 |
0.343 |
|
| 2005 |
Fukunaga R, Yokoyama S. Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain. The Journal of Biological Chemistry. 280: 29937-45. PMID 15970591 DOI: 10.1074/Jbc.M502668200 |
0.352 |
|
| 2005 |
Ebihara A, Okamoto A, Kousumi Y, Yamamoto H, Masui R, Ueyama N, Yokoyama S, Kuramitsu S. Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8 Journal of Structural and Functional Genomics. 6: 21-32. PMID 15965735 DOI: 10.1007/s10969-005-1103-x |
0.308 |
|
| 2005 |
Arai R, Kukimoto-Niino M, Uda-Tochio H, Morita S, Uchikubo-Kamo T, Akasaka R, Etou Y, Hayashizaki Y, Kigawa T, Terada T, Shirouzu M, Yokoyama S. Crystal structure of an enhancer of rudimentary homolog (ERH) at 2.1 Angstroms resolution. Protein Science : a Publication of the Protein Society. 14: 1888-93. PMID 15937287 DOI: 10.1110/ps.051484505 |
0.366 |
|
| 2005 |
Kinebuchi T, Kagawa W, Kurumizaka H, Yokoyama S. Role of the N-terminal domain of the human DMC1 protein in octamer formation and DNA binding. The Journal of Biological Chemistry. 280: 28382-7. PMID 15917243 DOI: 10.1074/jbc.M503372200 |
0.319 |
|
| 2005 |
Kato-Murayama M, Bessho Y, Shirouzu M, Yokoyama S. Crystal structure of the RNA 2'-phosphotransferase from Aeropyrum pernix K1. Journal of Molecular Biology. 348: 295-305. PMID 15811369 DOI: 10.1016/j.jmb.2005.02.049 |
0.417 |
|
| 2005 |
Kurimoto K, Muto Y, Obayashi N, Terada T, Shirouzu M, Yabuki T, Aoki M, Seki E, Matsuda T, Kigawa T, Okumura H, Tanaka A, Shibata N, Kashikawa M, Agata K, ... Yokoyama S, et al. Crystal structure of the N-terminal RecA-like domain of a DEAD-box RNA helicase, the Dugesia japonica vasa-like gene B protein. Journal of Structural Biology. 150: 58-68. PMID 15797730 DOI: 10.1016/J.Jsb.2005.01.006 |
0.369 |
|
| 2005 |
Handa N, Terada T, Doi-Katayama Y, Hirota H, Tame JR, Park SY, Kuramitsu S, Shirouzu M, Yokoyama S. Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8. Protein Science : a Publication of the Protein Society. 14: 1004-10. PMID 15741337 DOI: 10.1110/ps.041183305 |
0.326 |
|
| 2005 |
Ishii R, Minagawa A, Takaku H, Takagi M, Nashimoto M, Yokoyama S. Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima. The Journal of Biological Chemistry. 280: 14138-44. PMID 15701599 DOI: 10.1074/jbc.M500355200 |
0.327 |
|
| 2005 |
Kukimoto-Niino M, Shibata R, Murayama K, Hamana H, Nishimoto M, Bessho Y, Terada T, Shirouzu M, Kuramitsu S, Yokoyama S. Crystal structure of a predicted phosphoribosyltransferase (TT1426) from Thermus thermophilus HB8 at 2.01 A resolution. Protein Science : a Publication of the Protein Society. 14: 823-7. PMID 15689504 DOI: 10.1110/ps.041229405 |
0.405 |
|
| 2005 |
Kuratani M, Ishii R, Bessho Y, Fukunaga R, Sengoku T, Shirouzu M, Sekine S, Yokoyama S. Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus. The Journal of Biological Chemistry. 280: 16002-8. PMID 15677468 DOI: 10.1074/Jbc.M414541200 |
0.377 |
|
| 2005 |
Fukunaga R, Yokoyama S. Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation. Journal of Molecular Biology. 346: 57-71. PMID 15663927 DOI: 10.1016/J.Jmb.2004.11.060 |
0.324 |
|
| 2005 |
Watanabe K, Nureki O, Fukai S, Ishii R, Okamoto H, Yokoyama S, Endo Y, Hori H. Roles of conserved amino acid sequence motifs in the SpoU (TrmH) RNA methyltransferase family. The Journal of Biological Chemistry. 280: 10368-77. PMID 15637073 DOI: 10.1074/jbc.M411209200 |
0.535 |
|
| 2004 |
Kobayashi T, Takimura T, Sekine R, Kelly VP, Kamata K, Sakamoto K, Nishimura S, Yokoyama S. Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase. Journal of Molecular Biology. 346: 105-17. PMID 15663931 DOI: 10.1016/j.jmb.2004.11.034 |
0.347 |
|
| 2004 |
Kukimoto-Niino M, Murayama K, Kato-Murayama M, Idaka M, Bessho Y, Tatsuguchi A, Ushikoshi-Nakayama R, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S. Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8. Protein Science : a Publication of the Protein Society. 13: 3038-42. PMID 15459330 DOI: 10.1110/ps.041012404 |
0.357 |
|
| 2004 |
Fukunaga R, Yokoyama S. Crystallization and preliminary X-ray crystallographic study of the editing domain of Thermus thermophilus isoleucyl-tRNA synthetase complexed with pre- and post-transfer editing-substrate analogues. Acta Crystallographica. Section D, Biological Crystallography. 60: 1900-2. PMID 15388946 DOI: 10.1107/S0907444904019511 |
0.328 |
|
| 2004 |
Wang H, Takemoto CH, Murayama K, Sakai H, Tatsuguchi A, Terada T, Shirouzu M, Kuramitsu S, Yokoyama S. Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8. Protein Science : a Publication of the Protein Society. 13: 2806-10. PMID 15340170 DOI: 10.1110/ps.04864904 |
0.302 |
|
| 2004 |
Nameki N, Yoneyama M, Koshiba S, Tochio N, Inoue M, Seki E, Matsuda T, Tomo Y, Harada T, Saito K, Kobayashi N, Yabuki T, Aoki M, Nunokawa E, Matsuda N, ... ... Yokoyama S, et al. Solution structure of the RWD domain of the mouse GCN2 protein. Protein Science : a Publication of the Protein Society. 13: 2089-100. PMID 15273307 DOI: 10.1110/Ps.04751804 |
0.306 |
|
| 2004 |
Okubo S, Hara F, Tsuchida Y, Shimotakahara S, Suzuki S, Hatanaka H, Yokoyama S, Tanaka H, Yasuda H, Shindo H. NMR structure of the N-terminal domain of SUMO ligase PIAS1 and its interaction with tumor suppressor p53 and A/T-rich DNA oligomers. The Journal of Biological Chemistry. 279: 31455-61. PMID 15133049 DOI: 10.1074/jbc.M403561200 |
0.307 |
|
| 2004 |
Artsimovitch I, Patlan V, Sekine S, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S, Vassylyev DG. Structural basis for transcription regulation by alarmone ppGpp. Cell. 117: 299-310. PMID 15109491 DOI: 10.1016/S0092-8674(04)00401-5 |
0.302 |
|
| 2004 |
Wada T, Shirouzu M, Terada T, Kamewari Y, Park SY, Tame JR, Kuramitsu S, Yokoyama S. Crystal structure of the conserved hypothetical protein TT1380 from Thermus thermophilus HB8. Proteins. 55: 778-80. PMID 15103643 DOI: 10.1002/prot.20122 |
0.328 |
|
| 2004 |
Katsura Y, Shirouzu M, Yamaguchi H, Ishitani R, Nureki O, Kuramitsu S, Hayashi H, Yokoyama S. Crystal structure of a putative aspartate aminotransferase belonging to subgroup IV. Proteins. 55: 487-92. PMID 15103612 DOI: 10.1002/prot.20020 |
0.532 |
|
| 2004 |
Nureki O, Watanabe K, Fukai S, Ishii R, Endo Y, Hori H, Yokoyama S. Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure (London, England : 1993). 12: 593-602. PMID 15062082 DOI: 10.1016/j.str.2004.03.003 |
0.554 |
|
| 2004 |
Tahirov TH, Inagaki E, Ohshima N, Kitao T, Kuroishi C, Ukita Y, Takio K, Kobayashi M, Kuramitsu S, Yokoyama S, Miyano M. Crystal structure of purine nucleoside phosphorylase from Thermus thermophilus. Journal of Molecular Biology. 337: 1149-60. PMID 15046984 DOI: 10.1016/j.jmb.2004.02.016 |
0.31 |
|
| 2004 |
Kukimoto-Niino M, Murayama K, Inoue M, Terada T, Tame JR, Kuramitsu S, Shirouzu M, Yokoyama S. Crystal structure of the GTP-binding protein Obg from Thermus thermophilus HB8. Journal of Molecular Biology. 337: 761-70. PMID 15019792 DOI: 10.1016/j.jmb.2004.01.047 |
0.321 |
|
| 2004 |
Ito N, Nureki O, Shirouzu M, Yokoyama S, Hanaoka F. Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis. Genes to Cells : Devoted to Molecular & Cellular Mechanisms. 8: 913-23. PMID 14750947 DOI: 10.1111/j.1365-2443.2003.00693.x |
0.45 |
|
| 2004 |
Sengoku T, Nureki O, Dohmae N, Nakamura A, Yokoyama S. Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue. Acta Crystallographica. Section D, Biological Crystallography. 60: 320-2. PMID 14747711 DOI: 10.1107/S0907444903025897 |
0.53 |
|
| 2004 |
Kise Y, Lee SW, Park SG, Fukai S, Sengoku T, Ishii R, Yokoyama S, Kim S, Nureki O. A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase. Nature Structural & Molecular Biology. 11: 149-56. PMID 14730354 DOI: 10.1038/nsmb722 |
0.495 |
|
| 2004 |
Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe M, Hiraga S, Yokoyama S. Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein. Nucleic Acids Research. 32: 82-92. PMID 14704346 DOI: 10.1093/nar/gkh173 |
0.483 |
|
| 2004 |
Fukunaga R, Fukai S, Ishitani R, Nureki O, Yokoyama S. Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine. The Journal of Biological Chemistry. 279: 8396-402. PMID 14672940 DOI: 10.1074/Jbc.M312830200 |
0.508 |
|
| 2004 |
Seto A, Shirouzu M, Terada T, Murayama K, Kuramitsu S, Yokoyama S. Crystal structure of a hypothetical protein, TT1725, from Thermus thermophilus HB8 at 1.7 A resolution. Proteins. 53: 768-71. PMID 14579367 DOI: 10.1002/prot.10412 |
0.313 |
|
| 2004 |
Handa N, Terada T, Kamewari Y, Hamana H, Tame JR, Park SY, Kinoshita K, Ota M, Nakamura H, Kuramitsu S, Shirouzu M, Yokoyama S. Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8. Protein Science : a Publication of the Protein Society. 12: 1621-32. PMID 12876312 DOI: 10.1110/gad.03104003 |
0.392 |
|
| 2003 |
Okabe M, Tomita K, Ishitani R, Ishii R, Takeuchi N, Arisaka F, Nureki O, Yokoyama S. Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure. The Embo Journal. 22: 5918-27. PMID 14592988 DOI: 10.1093/Emboj/Cdg563 |
0.488 |
|
| 2003 |
Polycarpo C, Ambrogelly A, Ruan B, Tumbula-Hansen D, Ataide SF, Ishitani R, Yokoyama S, Nureki O, Ibba M, Söll D. Activation of the pyrrolysine suppressor tRNA requires formation of a ternary complex with class I and class II lysyl-tRNA synthetases. Molecular Cell. 12: 287-94. PMID 14536069 DOI: 10.1016/S1097-2765(03)00280-6 |
0.47 |
|
| 2003 |
Tawaramoto MS, Park SY, Tanaka Y, Nureki O, Kurumizaka H, Yokoyama S. Crystal structure of the human centromere protein B (CENP-B) dimerization domain at 1.65-A resolution. The Journal of Biological Chemistry. 278: 51454-61. PMID 14522975 DOI: 10.1074/jbc.M310388200 |
0.486 |
|
| 2003 |
Sakai H, Vassylyeva MN, Matsuura T, Sekine Si, Gotoh K, Nishiyama M, Terada T, Shirouzu M, Kuramitsu S, Vassylyev DG, Yokoyama S. Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8. Journal of Molecular Biology. 332: 729-40. PMID 12963379 DOI: 10.1016/s0022-2836(03)00946-x |
0.335 |
|
| 2003 |
Kurumizaka H, Enomoto R, Nakada M, Eda K, Yokoyama S, Shibata T. Region and amino acid residues required for Rad51C binding in the human Xrcc3 protein. Nucleic Acids Research. 31: 4041-50. PMID 12853621 DOI: 10.1093/nar/gkg442 |
0.3 |
|
| 2003 |
Kigawa T, Yamaguchi-Nunokawa E, Kodama K, Matsuda T, Yabuki T, Matsuda N, Ishitani R, Nureki O, Yokoyama S. Selenomethionine incorporation into a protein by cell-free synthesis. Journal of Structural and Functional Genomics. 2: 29-35. PMID 12836672 DOI: 10.1023/a:1013203532303 |
0.479 |
|
| 2003 |
Koshiba S, Kigawa T, Kikuchi A, Yokoyama S. Solution structure of the epsin N-terminal homology (ENTH) domain of human epsin. Journal of Structural and Functional Genomics. 2: 1-8. PMID 12836669 DOI: 10.1023/a:1011397007366 |
0.302 |
|
| 2003 |
Wada T, Shirouzu M, Terada T, Ishizuka Y, Matsuda T, Kigawa T, Kuramitsu S, Park SY, Tame JR, Yokoyama S. Structure of a conserved CoA-binding protein synthesized by a cell-free system. Acta Crystallographica. Section D, Biological Crystallography. 59: 1213-8. PMID 12832765 |
0.369 |
|
| 2003 |
Kobayashi T, Nureki O, Ishitani R, Yaremchuk A, Tukalo M, Cusack S, Sakamoto K, Yokoyama S. Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. Nature Structural Biology. 10: 425-32. PMID 12754495 DOI: 10.2142/Biophys.43.S94_1 |
0.518 |
|
| 2003 |
Ishii R, Nureki O, Yokoyama S. Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus. The Journal of Biological Chemistry. 278: 32397-404. PMID 12746447 DOI: 10.1074/jbc.M300639200 |
0.536 |
|
| 2003 |
Ishitani R, Nureki O, Nameki N, Okada N, Nishimura S, Yokoyama S. Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell. 113: 383-94. PMID 12732145 DOI: 10.1016/s0092-8674(03)00280-0 |
0.528 |
|
| 2003 |
Fujikawa N, Kurumizaka H, Nureki O, Terada T, Shirouzu M, Katayama T, Yokoyama S. Structural basis of replication origin recognition by the DnaA protein. Nucleic Acids Research. 31: 2077-86. PMID 12682358 DOI: 10.1093/nar/gkg309 |
0.497 |
|
| 2003 |
Someya T, Nameki N, Hosoi H, Suzuki S, Hatanaka H, Fujii M, Terada T, Shirouzu M, Inoue Y, Shibata T, Kuramitsu S, Yokoyama S, Kawai G, James TL. Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus Febs Letters. 535: 94-100. PMID 12560085 DOI: 10.1016/S0014-5793(02)03880-2 |
0.303 |
|
| 2003 |
Fukai S, Nureki O, Sekine S, Shimada A, Vassylyev DG, Yokoyama S. Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase. Rna (New York, N.Y.). 9: 100-11. PMID 12554880 DOI: 10.1261/rna.2760703 |
0.509 |
|
| 2003 |
Sekine S, Nureki O, Dubois DY, Bernier S, Chênevert R, Lapointe J, Vassylyev DG, Yokoyama S. ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. The Embo Journal. 22: 676-88. PMID 12554668 DOI: 10.1093/Emboj/Cdg053 |
0.496 |
|
| 2002 |
Tahirov TH, Temiakov D, Anikin M, Patlan V, McAllister WT, Vassylyev DG, Yokoyama S. Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution. Nature. 420: 43-50. PMID 12422209 DOI: 10.1038/Nature01129 |
0.309 |
|
| 2002 |
Ogiso H, Ishitani R, Nureki O, Fukai S, Yamanaka M, Kim JH, Saito K, Sakamoto A, Inoue M, Shirouzu M, Yokoyama S. Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains. Cell. 110: 775-87. PMID 12297050 DOI: 10.1016/S0092-8674(02)00963-7 |
0.473 |
|
| 2002 |
Vassylyeva MN, Lee J, Sekine SI, Laptenko O, Kuramitsu S, Shibata T, Inoue Y, Borukhov S, Vassylyev DG, Yokoyama S. Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus. Acta Crystallographica. Section D, Biological Crystallography. 58: 1497-500. PMID 12198314 DOI: 10.1107/S0907444902011770 |
0.314 |
|
| 2002 |
Kagawa W, Kurumizaka H, Ishitani R, Fukai S, Nureki O, Shibata T, Yokoyama S. Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form. Molecular Cell. 10: 359-71. PMID 12191481 DOI: 10.1016/s1097-2765(02)00587-7 |
0.534 |
|
| 2002 |
Nureki O, Shirouzu M, Hashimoto K, Ishitani R, Terada T, Tamakoshi M, Oshima T, Chijimatsu M, Takio K, Vassylyev DG, Shibata T, Inoue Y, Kuramitsu S, Yokoyama S. An enzyme with a deep trefoil knot for the active-site architecture. Acta Crystallographica. Section D, Biological Crystallography. 58: 1129-37. PMID 12077432 DOI: 10.1107/s0907444902006601 |
0.553 |
|
| 2002 |
Ishitani R, Nureki O, Fukai S, Kijimoto T, Nameki N, Watanabe M, Kondo H, Sekine M, Okada N, Nishimura S, Yokoyama S. Crystal structure of archaeosine tRNA-guanine transglycosylase. Journal of Molecular Biology. 318: 665-77. PMID 12054814 DOI: 10.1016/S0022-2836(02)00090-6 |
0.599 |
|
| 2002 |
Vassylyev DG, Sekine S, Laptenko O, Lee J, Vassylyeva MN, Borukhov S, Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature. 417: 712-9. PMID 12000971 DOI: 10.1038/nature752 |
0.358 |
|
| 2002 |
Terada T, Nureki O, Ishitani R, Ambrogelly A, Ibba M, Söll D, Yokoyama S. Functional convergence of two lysyl-tRNA synthetases with unrelated topologies. Nature Structural Biology. 9: 257-62. PMID 11887185 DOI: 10.1038/Nsb777 |
0.519 |
|
| 2002 |
Hendrickson TL, Nomanbhoy TK, De Crécy-Lagard V, Fukai S, Nureki O, Yokoyama S, Schimmel P. Mutational separation of two pathways for editing by a class I tRNA synthetase Molecular Cell. 9: 353-362. PMID 11864608 DOI: 10.1016/S1097-2765(02)00449-5 |
0.503 |
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