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 Escherichia Coli Holoenzymes Bacterial Rna Dna Rna X Rays Crystal Structure Sugars Transcription Mycobacterium Tuberculosis Recycling Mutation Deoxyribonucleic Acid Bacteria Ribosomal Rna Catalytic Domain Rifampin Lycorine Growth Tuberculosis Rifamycin Sv Antiviral Agents Molecule Food

Most Recent Publications

Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay

Anoop Narayanan, Manju Narwal, Sydney A. Majowicz, Carmine Varricchio, Shay A. Toner, Carlo Ballatore, Andrea Brancale, Katsuhiko S. Murakami, Joyce Jose, 2022, Communications Biology

Author Correction: Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity (Nature Communications, (2022), 13, 1, (4624), 10.1038/s41467-022-32079-5)

Lidiya Lisitskaya, Yeonoh Shin, Aleksei Agapov, Anna Olina, Ekaterina Kropocheva, Sergei Ryazansky, Alexei A. Aravin, Daria Esyunina, Katsuhiko S. Murakami, Andrey Kulbachinskiy, 2022, Nature Communications

Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity

Lidiya Lisitskaya, Yeonoh Shin, Aleksei Agapov, Anna Olina, Ekaterina Kropocheva, Sergei Ryazansky, Alexei A. Aravin, Daria Esyunina, Katsuhiko S. Murakami, Andrey Kulbachinskiy, 2022, Nature Communications

Optimization of Benzoxazinorifamycins to Improve Mycobacterium tuberculosis RNA Polymerase Inhibition and Treatment of Tuberculosis

Walajapet Rajeswaran, Shireen R. Ashkar, Pil H. Lee, Larisa Yeomans, Yeonoh Shin, Scott G. Franzblau, Katsuhiko S. Murakami, Hollis D. Showalter, George A. Garcia, 2022, ACS Infectious Diseases on p. 1422-1438

Optimization of Benzoxazinorifamycins to Minimize hPXR Activation for the Treatment of Tuberculosis and HIV Coinfection

Shireen R. Ashkar, Walajapet Rajeswaran, Pil H. Lee, Larisa Yeomans, Claire M. Thrasher, Scott G. Franzblau, Katsuhiko S. Murakami, Hollis D. Showalter, George A. Garcia, 2022, ACS Infectious Diseases on p. 1408-1421

The structure and activities of the archaeal transcription termination factor Eta detail vulnerabilities of the transcription elongation complex

Craig J. Marshall, M. Zuhaib Qayyum, Julie E. Walker, Katsuhiko S. Murakami, Thomas J. Santangelo, 2022, Proceedings of the National Academy of Sciences of the United States of America

On the stability of stalled RNA polymerase and its removal by RapA

James R. Portman, M. Zuhaib Qayyum, Katsuhiko S. Murakami, Terence R. Strick, 2022, Nucleic Acids Research on p. 7396-7405

Structural basis of ribosomal RNA transcription regulation

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

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 RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli

M. Zuhaib Qayyum, Vadim Molodtsov, Andrew Renda, Katsuhiko S. Murakami, 2021, Journal of Biological Chemistry

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

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

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

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

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

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

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