Researcher Profile

Researcher Profile

Katsuhiko Murakami

Katsuhiko Murakami

Professor, Biochemistry & Molecular Biology
Scientific Program:Mechanisms of Carcinogenesis
kum14@psu.edu
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Research Interests

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

Recent Publications

2019

Black, SJ, Ozdemir, AY, Kashkina, E, Kent, T, Rusanov, T, Ristic, D, Shin, Y, Suma, A, Hoang, T, Chandramouly, G, Siddique, LA, Borisonnik, N, Sullivan-Reed, K, Mallon, JS, Skorski, T, Carnevale, V, Murakami, KS, Wyman, C & Pomerantz, RT 2019, 'Molecular basis of microhomology-mediated end-joining by purified full-length Polθ', Nature communications, vol. 10, no. 1, 4423. https://doi.org/10.1038/s41467-019-12272-9
Prakash, D, Iyer, PR, Suharti, S, Walters, KA, Santiago-Martinez, MG, Golbeck, JH, Murakami, KS & Ferry, JG 2019, 'Structure and function of an unusual flavodoxin from the domain Archaea', Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 51, pp. 25917-25922. https://doi.org/10.1073/pnas.1908578116

2018

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. https://doi.org/10.1016/j.molcel.2018.01.035
Sutherland, C & Murakami, KS 2018, 'An Introduction to the Structure and Function of the Catalytic Core Enzyme of Escherichia coli RNA Polymerase', EcoSal Plus, vol. 8, no. 1. https://doi.org/10.1128/ecosalplus.ESP-0004-2018
Narayanan, A, Vago, FS, Li, K, Qayyum, MZ, Yernool, D, Jiang, W & Murakami, KS 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. https://doi.org/10.1074/jbc.RA118.002161
Molodtsov, V & Murakami, KS 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. https://doi.org/10.1074/jbc.RA118.003447
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, KS & 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. https://doi.org/10.1016/j.molcel.2018.08.028
Pupov, D, Petushkov, I, Esyunina, D, Murakami, KS & 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. https://doi.org/10.1093/nar/gky919
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. https://doi.org/10.1016/j.bbagrm.2018.07.005

2017

Scharf, NT, Molodtsov, V, Kontos, A, Murakami, KS & 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. https://doi.org/10.1177/2472555216679994
Molodtsov, V, Scharf, NT, Stefan, MA, Garcia, GA & Murakami, KS 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. https://doi.org/10.1111/mmi.13606
Murakami, KS, 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. https://doi.org/10.1073/pnas.1702741114

2016

Yakhnin, AV, Murakami, KS & Babitzke, P 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. https://doi.org/10.1074/jbc.M115.704189
Gu, H, Yoshinari, S, Ghosh, R, Ignatochkina, AV, Gollnick, PD, Murakami, KS & 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. https://doi.org/10.1093/nar/gkw094

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