Biochemistry and Molecular Biology
Penn State Science
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Katsuhiko Murakami

Katsuhiko Murakami

Main Content

  • Professor of Biochemistry and Molecular Biology
006 Althouse Laboratory
University Park, PA 16802
Phone: (814) 865-2758

Research Interests

Structural and Mechanistic Enzymology of Prokaryotic RNA Polymerases

Graduate Programs


Research Summary

Gene expression is fundamental to all organisms and studying how the genetic code is expressed in molecular terms is critical to cell development and understanding diseases. Our research interests are centered on understanding the mechanism of gene expression, particularly how information stored in genomic DNA is transcribed into RNA by the enzyme RNA polymerase – the first step and the key control point in the gene expression and one of the most fundamental processes required for life. We apply X-ray crystallography and cryo-electron microscopy techniques to reveal three-dimensional structures of bacterial, archaeal and bacteriophage RNA polymerases for elucidating the mechanism of RNA transcription.

Selected Publications

Bacterial RNA polymerase:

  • Murakami, K.S., Shin, Y., Turnbough, C.L., Jr., and Molodtsov, V. (2017). X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway. Proc Natl Acad Sci U S A 114, 8211-8216.
  • Molodtsov, V., Scharf, N.T., Stefan, M.A., Garcia, G.A., and Murakami, K.S. (2017). Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis. Mol Microbiol 103, 1034-1045.
  • Basu, R.S., Warner, B.A., Molodtsov, V., Pupov, D., Esyunina, D., Fernandez-Tornero, C., Kulbachinskiy, A., and Murakami, K.S. (2014). Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme. J Biol Chem 289, 24549-24559.
  • Murakami, K.S. (2013). X-ray crystal structure of Escherichia coli RNA polymerase s70 holoenzyme. J Biol Chem 288, 9126-9134.


Archaeal RNA polymerase:


  • Jun, S.H., Hirata, A., Kanai, T., Santangelo, T.J., Imanaka, T., and Murakami, K.S. (2014). The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration. Nat Commun 5, 5132.
  • Klein, B.J., Bose, D., Baker, K.J., Yusoff, Z.M., Zhang, X., and Murakami, K.S. (2011). RNA polymerase and transcription elongation factor Spt4/5 complex structure. Proc Natl Acad Sci U S A 108, 546-550.
  • Hirata, A., Klein, B.J., and Murakami, K.S. (2008). The X-ray crystal structure of RNA polymerase from Archaea. Nature 451, 851-854.



Bacteriophage RNA polymerase:

  • Basu, R.S., and Murakami, K.S. (2013). Watching the bacteriophage N4 RNA polymerase transcription by time-dependent soak-trigger-freeze X-ray crystallography. J Biol Chem 288, 3305-3311.

  • Gleghorn, M.L., Davydova, E.K., Basu, R., Rothman-Denes, L.B., and Murakami, K.S. (2011). X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides. Proc Natl Acad Sci U S A 108, 3566-3571.

  • Gleghorn, M.L., Davydova, E.K., Rothman-Denes, L.B., and Murakami, K.S. (2008). Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase. Mol Cell 32, 707-717.

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