Researcher Profile

Researcher Profile

Katsuhiko Murakami

Katsuhiko Murakami

Professor, Biochemistry & Molecular Biology
Scientific Program:Mechanisms of Carcinogenesis
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Research Interests

  • DNA-Directed RNA Polymerases
  • DNA
  • Escherichia coli
  • X-Rays
  • Enzymes
  • Bacterial RNA
  • Proteins
  • Transcriptional Activation
  • Transcription Factors
  • Holoenzymes
  • RNA
  • Binding Sites

Recent Publications


Molodtsov, V, Sineva, EV, Zhang, L, Huang, X, Cashel, M, Ades, SE & Murakami, K 2018, 'Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA', Molecular cell, vol. 69, no. 5, pp. 828-839.e5.
Sutherland, C & Murakami, K 2018, 'An Introduction to the Structure and Function of the Catalytic Core Enzyme of Escherichia coli RNA Polymerase', EcoSal Plus, vol. 8, no. 1.
Narayanan, A, Vago, FS, Li, K, Qayyum, MZ, Yernool, D, Jiang, W & Murakami, K 2018, 'Cryo-EM structure of Escherichia coli 70 RNA polymerase and promoter DNA complex revealed a role of non-conserved region during the open complex formation', Journal of Biological Chemistry, vol. 293, no. 19, pp. 7367-7375.
Molodtsov, V & Murakami, K 2018, 'Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II' Journal of Biological Chemistry, vol. 293, no. 35, pp. 13616-13625.
Mosaei, H, Molodtsov, V, Kepplinger, B, Harbottle, J, Moon, CW, Jeeves, RE, Ceccaroni, L, Shin, Y, Morton-Laing, S, Marrs, ECL, Wills, C, Clegg, W, Yuzenkova, Y, Perry, JD, Bacon, J, Errington, J, Allenby, NEE, Hall, MJ, Murakami, K & Zenkin, N 2018, 'Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis', Molecular cell, vol. 72, no. 2, pp. 263-274.e5.
Pupov, D, Petushkov, I, Esyunina, D, Murakami, K & Kulbachinskiy, A 2018, 'Region 3.2 of the factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA', Nucleic acids research, vol. 46, no. 21, pp. 11477-11487.
Bruhn-Olszewska, B, Molodtsov, V, Sobala, M, Dylewski, M, Murakami, K, Cashel, M & Potrykus, K 2018, 'Structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites and for rrnB P1 promoter regulatory responses in vitro', Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, vol. 1861, no. 8, pp. 731-742.


Scharf, NT, Molodtsov, V, Kontos, A, Murakami, K & Garcia, GA 2017, 'Novel chemical scaffolds for inhibition of rifamycin-resistant RNA polymerase discovered from high-throughput screening', SLAS Discovery, vol. 22, no. 3, pp. 287-297.
Molodtsov, V, Scharf, NT, Stefan, MA, Garcia, GA & Murakami, K 2017, 'Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis', Molecular Microbiology, vol. 103, no. 6, pp. 1034-1045.
Murakami, K, Shin, Y, Turnbough, CL & Molodtsov, V 2017, 'X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway', Proceedings of the National Academy of Sciences of the United States of America, vol. 114, no. 31, pp. 8211-8216.


Yakhnin, AV, Murakami, K & Babitzke, PL 2016, 'NusG is a sequence-specific RNA polymerase pause factor that binds to the non-template DNA within the paused transcription bubble', Journal of Biological Chemistry, vol. 291, no. 10, pp. 5299-5308.
Gu, H, Yoshinari, S, Ghosh, R, Ignatochkina, AV, Gollnick, PD, Murakami, K & Ho, CK 2016, 'Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis', Nucleic acids research, vol. 44, no. 5, pp. 2337-2347.


Hauryliuk, V, Atkinson, GC, Murakami, K, Tenson, T & Gerdes, K 2015, 'Recent functional insights into the role of (p)ppGpp in bacterial physiology', Nature Reviews Microbiology, vol. 13, no. 5, pp. 298-309.
Murakami, K 2015, 'Structural biology of bacterial RNA polymerase', Biomolecules, vol. 5, no. 2, pp. 848-864.
Yang, Y, Darbari, VC, Zhang, N, Lu, D, Glyde, R, Wang, YP, Winkelman, JT, Gourse, RL, Murakami, K, Buck, M & Zhang, X 2015, 'Structures of the RNA polymerase-σ54 reveal new and conserved regulatory strategies', Science, vol. 349, no. 6250, pp. 882-885.
Molodtsov, V, Fleming, PR, Eyermann, CJ, Ferguson, AD, Foulk, MA, McKinney, DC, Masse, CE, Buurman, ET & Murakami, K 2015, 'X-ray Crystal Structures of Escherichia coli RNA Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with an Improved Fraction Unbound to Human Plasma Protein', Journal of Medicinal Chemistry, vol. 58, no. 7, pp. 3156-3171.

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