Katsuhiko Murakami

Professor of Biochemistry and Molecular Biology

Katsuhiko Murakami

Research Summary

Structural and Mechanistic Enzymology of Prokaryotic RNA Polymerases

Huck Affiliations

Links

Publication Tags

Dna Directed Rna Polymerases Dna Bacterial Rna Rna Holoenzymes Escherichia Coli Deoxyribonucleic Acid Transcription X Rays Proteins Sugars Nucleic Acids Protein X Ray Crystallography Bacteria Mycobacterium Tuberculosis Joining Mutation Communication Polytetrafluoroethylene Crystal Structure Rifampin Ribosomal Rna Substrates Cryo Electron Microscopy

Most Recent Papers

The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases

Janne J. Mäkinen, Yeonoh Shin, Eeva Vieras, Pasi Virta, Mikko Metsä-Ketelä, Katsuhiko S. Murakami, Georgiy A. Belogurov, 2021, Nature Communications

Structural basis of ribosomal RNA transcription regulation

Yeonoh Shin, M. Zuhaib Qayyum, Danil Pupov, Daria Esyunina, Andrey Kulbachinskiy, Katsuhiko S. Murakami, 2021, Nature Communications

Watching the bacterial RNA polymerase transcription reaction by time-dependent soak-trigger-freeze X-ray crystallography

Yeonoh Shin, Katsuhiko S. Murakami, 2021, on p. 305-314

Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase

Tomáš Kouba, Tomáš Koval’, Petra Sudzinová, Jiří Pospíšil, Barbora Brezovská, Jarmila Hnilicová, Hana Šanderová, Martina Janoušková, Michaela Šiková, Petr Halada, Michal Sýkora, Ivan Barvík, Jiří Nováček, Mária Trundová, Jarmila Dušková, Tereza Skálová, URee R. Chon, Katsuhiko S. Murakami, Jan Dohnálek, Libor Krásný, 2020, Nature Communications

Publisher Correction

Samuel J. Black, Ahmet Y. Ozdemir, Ekaterina Kashkina, Tatiana Kent, Timur Rusanov, Dejan Ristic, Yeonoh Shin, Antonio Suma, Trung Hoang, Gurushankar Chandramouly, Labiba A. Siddique, Nikita Borisonnik, Katherine Sullivan-Reed, Joseph S. Mallon, Tomasz Skorski, Vincenzo Carnevale, Katsuhiko S. Murakami, Claire Wyman, Richard T. Pomerantz, 2020, Nature Communications

Direct binding of TFEα opens DNA binding cleft of RNA polymerase

Sung Hoon Jun, Jaekyung Hyun, Jeong Seok Cha, Hoyoung Kim, Michael S. Bartlett, Hyun Soo Cho, Katsuhiko S. Murakami, 2020, Nature Communications

Evaluation of Bacterial RNA Polymerase Inhibitors in a Staphylococcus aureus-Based Wound Infection Model in SKH1 Mice

Jörg Haupenthal, Yannik Kautz, Walid A.M. Elgaher, Linda Pätzold, Teresa Röhrig, Matthias W. Laschke, Thomas Tschernig, Anna K.H. Hirsch, Vadim Molodtsov, Katsuhiko S. Murakami, Rolf W. Hartmann, Markus Bischoff, 2020, ACS Infectious Diseases on p. 2573-2581

Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase

Yeonoh Shin, Mark Hedglin, Katsuhiko S. Murakami, 2020, Nucleic Acids Research on p. 2144-2155

Structure and function of an unusual flavodoxin from the domain Archaea

Divya Prakash, Prashanti R. Iyer, Suharti Suharti, Karim A. Walters, Michel Geovanni Santiago-Martinez, John H. Golbeck, Katsuhiko S. Murakami, James G. Ferry, 2019, Proceedings of the National Academy of Sciences of the United States of America on p. 25917-25922

Molecular basis of microhomology-mediated end-joining by purified full-length Polθ

Samuel J. Black, Ahmet Y. Ozdemir, Ekaterina Kashkina, Tatiana Kent, Timur Rusanov, Dejan Ristic, Yeonoh Shin, Antonio Suma, Trung Hoang, Gurushankar Chandramouly, Labiba A. Siddique, Nikita Borisonnik, Katherine Sullivan-Reed, Joseph S. Mallon, Tomasz Skorski, Vincenzo Carnevale, Katsuhiko S. Murakami, Claire Wyman, Richard T. Pomerantz, 2019, Nature Communications on p. 4423

Most-Cited Papers

Recent functional insights into the role of (p)ppGpp in bacterial physiology

Vasili Hauryliuk, Gemma C. Atkinson, Katsuhiko S. Murakami, Tanel Tenson, Kenn Gerdes, 2015, Nature Reviews Microbiology on p. 298-309

X-ray crystal structure of escherichia coli RNA polymerase σ<sup>70</sup> holoenzyme

Katsuhiko S. Murakami, 2013, Journal of Biological Chemistry on p. 9126-9134

Differential regulation by ppGpp versus pppGpp in Escherichia coli

Undine Mechold, Katarzyna Potrykus, Helen Murphy, Katsuhiko S. Murakami, Michael Cashel, 2013, Nucleic Acids Research on p. 6175-6189

Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme

Ritwika S. Basu, Brittany A. Warner, Vadim Molodtsov, Danil Pupov, Daria Esyunina, Carlos Fernández-Tornero, Andrey Kulbachinskiy, Katsuhiko S. Murakami, 2014, Journal of Biological Chemistry on p. 24549-24559

Structural biology of bacterial RNA polymerase

Katsuhiko S. Murakami, 2015, Biomolecules on p. 848-864

Fitness costs of rifampicin resistance in Mycobacterium tuberculosis are amplified under conditions of nutrient starvation and compensated by mutation in the β′ subunit of RNA polymerase

Taeksun Song, Yumi Park, Isdore Chola Shamputa, Sunghwa Seo, Sun Young Lee, Han Seung Jeon, Hongjo Choi, Myungsun Lee, Richard J. Glynne, S. Whitney Barnes, John R. Walker, Serge Batalov, Karina Yusim, Shihai Feng, Chang Shung Tung, James Theiler, Laura E. Via, Helena I.M. Boshoff, Katsuhiko S. Murakami, Bette Korber, Clifton E. Barry, Sang Nae Cho, 2014, Molecular Microbiology on p. 1106-1119

Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA

Vadim Molodtsov, Elena Sineva, Lu Zhang, Xuhui Huang, Michael Cashel, Sarah E. Ades, Katsuhiko S. Murakami, 2018, Molecular Cell on p. 828-839.e5

Structures of the RNA polymerase-σ<sup>54</sup> reveal new and conserved regulatory strategies

Yun Yang, Vidya C. Darbari, Nan Zhang, Duo Lu, Robert Glyde, Yi Ping Wang, Jared T. Winkelman, Richard L. Gourse, Katsuhiko S. Murakami, Martin Buck, Xiaodong Zhang, 2015, Science on p. 882-885

Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis

Vadim Molodtsov, Nathan T. Scharf, Maxwell A. Stefan, George A. Garcia, Katsuhiko S. Murakami, 2017, Molecular Microbiology on p. 1034-1045

X-ray crystal structures of the Escherichia coli RNA polymerase in complex with benzoxazinorifamycins

Vadim Molodtsov, Irosha N. Nawarathne, Nathan T. Scharf, Paul D. Kirchhoff, H. D.Hollis Showalter, George A. Garcia, Katsuhiko S. Murakami, 2013, Journal of Medicinal Chemistry on p. 4758-4763