Affiliation: Pennsylvania State University
Murakami K, Davydova E, Rothman Denes L. X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase. Proc Natl Acad Sci U S A. 2008;105:5046-51 pubmed publisher
Murakami K, Shin Y, Turnbough C, Molodtsov V. X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway. Proc Natl Acad Sci U S A. 2017;114:8211-8216 pubmed publisher
..Nascent transcripts containing reiteratively added G residues are eventually extended by nonreiterative transcription, revealing an atypical pathway for the formation of a transcription elongation complex. ..
Mosaei H, Molodtsov V, Kepplinger B, Harbottle J, Moon C, Jeeves R, et al
. Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis. Mol Cell. 2018;72:263-274.e5 pubmed publisher
..Previous ansa-chain modifications in the rifamycin series have proven unsuccessful. Thus, KglA represents a key starting point for the development of a new class of ansa-chain derivatized ansamycins to tackle rifampicin resistance. ..
Molodtsov V, Murakami K. Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II. J Biol Chem. 2018;293:13616-13625 pubmed publisher
..This work establishes a structural basis for studying mechanistic aspects of transcription by factor-dependent minimum RNAP. ..
Murakami K. Structural biology of bacterial RNA polymerase. Biomolecules. 2015;5:848-64 pubmed publisher
Narayanan A, Vago F, Li K, Qayyum M, Yernool D, Jiang W, et al
. 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. J Biol Chem. 2018;293:7367-7375 pubmed publisher
..We propose that the ?NCR and DNA interaction is conserved in proteobacteria, and RNAP in other bacteria replaces its role with a transcription factor. ..
Bruhn Olszewska B, Molodtsov V, Sobala M, Dylewski M, Murakami K, Cashel M, et al
. 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. Biochim Biophys Acta Gene Regul Mech. 2018;1861:731-742 pubmed publisher
..Our observations underscore the importance of the (p)ppNpp's purine nucleobase for interactions with RNAP, which may lead to a better fundamental understanding of (p)ppGpp regulation of RNAP activity. ..
Molodtsov V, Sineva E, Zhang L, Huang X, Cashel M, Ades S, et al
. Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA. Mol Cell. 2018;69:828-839.e5 pubmed publisher
..This work establishes a structural basis for understanding the pleiotropic effects of DksA and ppGpp on transcriptional regulation in proteobacteria. ..
Murakami K. X-ray crystal structure of Escherichia coli RNA polymerase ?70 holoenzyme. J Biol Chem. 2013;288:9126-34 pubmed publisher
..E. coli RNAP crystals can be prepared from a convenient overexpression system, allowing further structural studies of bacterial RNAP mutants, including functionally deficient and antibiotic-resistant RNAPs...