K. Murakami

发表

Complete sequencing and characterization of 21,243 full-length human cDNAs

N. Nomura, Y. Masuho, H. Hishigaki, 2004, Nature Genetics.

Bacterial RNA polymerases: the wholo story.

K. Murakami, S. Darst, 2003, Current opinion in structural biology.

Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å Resolution

K. Murakami, S. Darst, S. Masuda, 2002, Science.

Structural Basis of Transcription Initiation: An RNA Polymerase Holoenzyme-DNA Complex

K. Murakami, S. Darst, E. Campbell, 2002, Science.

Recent functional insights into the role of (p)ppGpp in bacterial physiology

Tanel Tenson, Gemma C. Atkinson, K. Murakami, 2015, Nature Reviews Microbiology.

Mapping the σ70 subunit contact sites on Escherichia coli RNA polymerase with a σ70-conjugated chemical protease

Akira Ishihama, K. Murakami, N. Fujita, 1998 .

Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors.

K. Murakami, S. Busby, A. Ishihama, 1997, Proceedings of the National Academy of Sciences of the United States of America.

Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions

K. Nakai, K. Murakami, T. Gojobori, 2008, BMC Genomics.

Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA.

K. Murakami, Xuhui Huang, M. Cashel, 2018, Molecular cell.

Allosteric effector ppGpp potentiates the inhibition of transcript initiation by DksA

K. Murakami, Xuhui Huang, M. Cashel, 2017, bioRxiv.

c-Ets-1 protein is hyperphosphorylated during mitosis.

K. Murakami, R. Fisher, T. Papas, 1993, Oncogene.

Recruitment of σ54-RNA Polymerase to the Pu Promoter of Pseudomonas putida through Integration Host Factor-mediated Positioning Switch of α Subunit Carboxyl-terminal Domain on an UP-like Element*

V. de Lorenzo, K. Murakami, A. Ishihama, 2003, Journal of Biological Chemistry.

Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis

K. Murakami, J. Errington, Yulia Yuzenkova, 2018, Molecular cell.

Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis

K. Murakami, J. Errington, Yulia Yuzenkova, 2018, Molecular cell.

Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis

K. Murakami, N. Scharf, G. Garcia, 2017, Molecular microbiology.

X-ray crystal structures of the Escherichia coli RNA polymerase in complex with benzoxazinorifamycins.

K. Murakami, H. Showalter, N. Scharf, 2013, Journal of medicinal chemistry.

RNA polymerase and transcription elongation factor Spt4/5 complex structure

K. Murakami, D. Bose, Xiaodong Zhang, 2010, Proceedings of the National Academy of Sciences.

NusG Is a Sequence-specific RNA Polymerase Pause Factor That Binds to the Non-template DNA within the Paused Transcription Bubble*

K. Murakami, P. Babitzke, A. Yakhnin, 2016, The Journal of Biological Chemistry.

Molecular basis of microhomology-mediated end-joining by purified full-length Polθ

K. Murakami, V. Carnevale, T. Skorski, 2019, Nature Communications.

BAC library construction and BAC end sequencing of five Drosophila species: the comparative map with the D. melanogaster genome.

M. Hattori, Y. Sakaki, K. Murakami, 2008, Genes & genetic systems.

Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase

K. Murakami, H. Šanderová, I. Barvík, 2020, Nature communications.

Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase

K. Murakami, H. Šanderová, I. Barvík, 2020, Nature Communications.

Crystal structures of the ADP and ATP bound forms of the Bacillus anti-sigma factor SpoIIAB in complex with the anti-anti-sigma SpoIIAA.

K. Murakami, S. Darst, E. Campbell, 2004, Journal of molecular biology.

The 3rd DBCLS BioHackathon : Improving life science with semantic web technologies

Akira R. Kinjo, Fumikazu Konishi, Hammad Afzal, 2013 .

Evaluation of Bacterial RNA Polymerase Inhibitors in a Staphylococcus aureus-based Wound-Infection Model in SKH1 Mice.

K. Murakami, R. Hartmann, M. Bischoff, 2020, ACS infectious diseases.

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

K. Murakami, A. Brancale, M. Narwal, 2022, Communications Biology.

MreA Functions in the Global Regulation of Methanogenic Pathways in Methanosarcina acetivorans

K. Murakami, J. Ferry, V. Vepachedu, 2012, mBio.

Co-overexpression of Escherichia coliRNA Polymerase Subunits Allows Isolation and Analysis of Mutant Enzymes Lacking Lineage-specific Sequence Insertions*

K. Murakami, R. Landick, I. Artsimovitch, 2003, The Journal of Biological Chemistry.

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

K. Murakami, T. Santangelo, C. Marshall, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Oxidative damage to cellular and isolated DNA by homocysteine: implications for carcinogenesis

K. Murakami, S. Oikawa, S. Kawanishi, 2003, Oncogene.

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

K. Murakami, A. Aravin, Sergei Ryazansky, 2022, Nature Communications.

Upstream interactions at the lambda pRM promoter are sequence nonspecific and activate the promoter to a lesser extent than an introduced UP element of an rRNA promoter

K. Murakami, A. Ishihama, P. Dehaseth, 1996, Journal of bacteriology.

Evaluation of Database Annotation to Determine Human Mitochondrial Proteins

K. Murakami, M. Sugita, 2018 .

Specific fluorescent labeling of two functional domains in RNA polymerase α subunit

K. Murakami, N. Fujita, A. Ishihama, 1998 .

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

K. Murakami, H. Showalter, S. Franzblau, 2022, ACS infectious diseases.

Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase

K. Murakami, P. Babitzke, R. Vishwakarma, 2022, bioRxiv.

Nature of DNA binding and RNA polymerase interaction of the Bordetella pertussis BvgA transcriptional activator at the fha promoter

K. Murakami, A. Ishihama, S. Stibitz, 1997, Journal of bacteriology.

Faculty Opinions recommendation of Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation.

K. Murakami, 2008 .

An Introduction to the Structure and Function of the Catalytic Core Enzyme of Escherichia coli RNA Polymerase

K. Murakami, C. Sutherland, 2018, EcoSal Plus.

H-InvDB release 6, a comprehensive annotation resource for human genes and transcripts

Yoshiharu Sato, Takuya Habara, Akihiro Matsuya, 2009 .

H-InvDB in 2009: extended database and data mining resources for human genes and transcripts

Katsuhiko Murakami, Yoshiharu Sato, Takuya Habara, 2009, Nucleic Acids Res..

SARS-CoV-2 polyprotein substrate regulates the stepwise Mpro cleavage reaction

K. Murakami, J. Armache, M. Narwal, 2022, bioRxiv.

Nucleic Acid Polymerases

K. Murakami, M. Trakselis, 2014, Nucleic Acids and Molecular Biology.

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.

K. Murakami, C. Eyermann, A. Ferguson, 2015, Journal of medicinal chemistry.

Structural Mechanism for Rifampicin Inhibition of Bacterial RNA Polymerase

Arkady Mustaev, Seth A. Darst, K. Murakami, 2001, Cell.

X-ray Crystal Structure of Escherichia coli RNA Polymerase σ70 Holoenzyme*

K. Murakami, Katsuhiko S. Murakami, 2013, The Journal of Biological Chemistry.

Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase

K. Murakami, P. Babitzke, R. Vishwakarma, 2022, bioRxiv.

Watching the bacterial RNA polymerase transcription reaction by time-dependent soak-trigger-freeze X-ray crystallography.

K. Murakami, Y. Shin, 2021, The Enzymes.

The X-ray crystal structure of RNA polymerase from Archaea

Akira Hirata, K. Murakami, Katsuhiko S. Murakami, 2008, Nature.

Structure and function of lineage-specific sequence insertions in the bacterial RNA polymerase beta' subunit.

K. Murakami, S. Darst, S. Masuda, 2005, Journal of molecular biology.

Structural Basis of Transcription Initiation by Bacterial RNA Polymerase Holoenzyme*

K. Murakami, C. Fernández‐Tornero, Ritwika S. Basu, 2014, The Journal of Biological Chemistry.

The X-ray crystal structure of RNA polymerase from Archaea

K. Murakami, A. Hirata, B. J. Klein, 2008, Nature.

Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II

K. Murakami, V. Molodtsov, 2018, The Journal of Biological Chemistry.

Watching the Bacteriophage N4 RNA Polymerase Transcription by Time-dependent Soak-trigger-freeze X-ray Crystallography*

K. Murakami, Katsuhiko S Murakami, Ritwika S Basu, 2012, The Journal of Biological Chemistry.

Crystallographic analysis of Thermus aquaticus RNA polymerase holoenzyme and a holoenzyme/promoter DNA complex.

K. Murakami, S. Darst, S. Masuda, 2003, Methods in enzymology.

Bacterial RNA polymerases: the wholo story.

J. Doudna, K. Murakami, S. Darst, 2003, Current opinion in structural biology.

Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase.

K. Murakami, L. Rothman-Denes, E. Davydova, 2008, Molecular cell.

The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases

K. Murakami, M. Metsä-Ketelä, G. Belogurov, 2020, Nature Communications.

Archaeal RNA polymerase and transcription regulation

K. Murakami, S. Jun, M. Reichlen, 2011, Critical reviews in biochemistry and molecular biology.

Archaeal RNA polymerase.

K. Murakami, A. Hirata, 2009, Current opinion in structural biology.

X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway

K. Murakami, C. Turnbough, V. Molodtsov, 2017, Proceedings of the National Academy of Sciences.

Structural Biology of Bacterial RNA Polymerase

K. Murakami, 2015, Biomolecules.

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

B. Korber, K. Murakami, J. Theiler, 2014, Molecular microbiology.

RNA Polymerase Reaction in Bacteria

K. Murakami, S. Jun, B. Warner, 2013 .

Holoenzyme 70 σ RNA Polymerase Escherichia coli X-ray Crystal Structure of Gene Regulation

K. Murakami, 2013 .

Inactivation of the Bacterial RNA Polymerase Due to Acquisition of Secondary Structure by the ω Subunit*

K. Murakami, D. Chatterji, A. A. Sardesai, 2013, The Journal of Biological Chemistry.

X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides

K. Murakami, L. Rothman-Denes, E. Davydova, 2011, Proceedings of the National Academy of Sciences.

Structural basis of ribosomal RNA transcription regulation

K. Murakami, Y. Shin, A. Kulbachinskiy, 2020, bioRxiv.

Region 3.2 of the σ factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA

K. Murakami, A. Kulbachinskiy, D. Esyunina, 2018, Nucleic acids research.

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.

K. Murakami, K. Potrykus, M. Cashel, 2018, Biochimica et biophysica acta. Gene regulatory mechanisms.

Catabolite activator protein: DNA binding and transcription activation.

D. Swigon, R. Ebright, H. Berman, 2004, Current opinion in structural biology.

, Subunit ω Secondary Structure by the Polymerase Due to Acquisition of Inactivation of the Bacterial RNA

K. Murakami, D. Chatterji, A. A. Sardesai, 2013 .

Cryo-EM structure of Escherichia coli σ70 RNA polymerase and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation

K. Murakami, Wen Jiang, D. Yernool, 2018, The Journal of Biological Chemistry.

Cryo-EM structure of Escherichia coli σ70 RNAP and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation

K. Murakami, Wen Jiang, D. Yernool, 2018, bioRxiv.

Structures of the RNA polymerase-σ54 reveal new and conserved regulatory strategies

Nan Zhang, Martin Buck, K. Murakami, 2015, Science.

The X-ray crystal structure of the euryarchaeal RNA polymerase in an open clamp configuration

Tadayuki Imanaka, Akira Hirata, K. Murakami, 2014, Nature Communications.

Direct binding of TFEα opens DNA binding cleft of RNA polymerase

K. Murakami, Hyun-soo Cho, J. Hyun, 2020, Nature Communications.

Protein-protein and protein-DNA interactions of σ70 region 4 involved in transcription activation by λcI

K. Murakami, S. Darst, A. Hochschild, 2002 .

Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase

K. Murakami, Y. Shin, Mark Hedglin, 2019, bioRxiv.

Bacteriophage RNA Polymerases

K. Murakami, R. Basu, 2014 .

Time-resolved events on the reaction pathway of transcript initiation by a single-subunit RNA polymerase: Raman crystallographic evidence.

K. Murakami, P. Carey, Yuanyuan Chen, 2011, Journal of the American Chemical Society.

Transcription | RNA Polymerase Reaction in Bacteria

K. Murakami, Y. Shin, M. Z. Qayyum, 2021, Encyclopedia of Biological Chemistry III.

X-ray crystal structur of Escherichia coli RNA polymerase sigma70 holoenzyme

K. Murakami, 2015 .

X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase

K. Murakami, L. Rothman-Denes, Elena K Davydova, 2008, Proceedings of the National Academy of Sciences.

PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from H-Invitational protein-protein interactions integrative dataset

Katsuhiko Murakami, Yoshiharu Sato, Mami Suzuki, 2012, BMC Systems Biology.

Differential regulation by ppGpp versus pppGpp in Escherichia coli

K. Murakami, K. Potrykus, M. Cashel, 2013, Nucleic acids research.

An Extracting System of Accurate ORFs from cDNA Sequences

Kouichi Kimura, T. Nishikawa, T. Sugiyama, 2002 .

An integrated analysis and database system for full-length cDNA.

K. Nagai, T. Ota, T. Nishikawa, 2000, Genome informatics. Workshop on Genome Informatics.

Structure and function of an unusual flavodoxin from the domain Archaea

K. Murakami, J. Ferry, M. G. Santiago-Martínez, 2019, Proceedings of the National Academy of Sciences.

Functional Analysis of the Three TATA Binding Protein Homologs in Methanosarcina acetivorans

K. Murakami, J. Ferry, M. Reichlen, 2010, Journal of bacteriology.

Biomarker discovery by integrated joint non-negative matrix factorization and pathway signature analyses

Kenta Nakai, Naoya Fujita, K. Nakai, 2018, Scientific Reports.

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Akira R. Kinjo, Yue Wang, Katsuhiko Murakami, 2019, F1000Research.

Introduction to Nucleic Acid Polymerases: Families, Themes, and Mechanisms

K. Murakami, M. Trakselis, 2014 .

Complex formation between lamin A and the retinoblastoma gene product: identification of the domain on lamin A required for its interaction.

K. Murakami, H. Enomoto, T. Ozaki, 1994, Oncogene.

Comprehensive transcription terminator atlas for Bacillus subtilis

K. Murakami, M. Kashlev, P. Babitzke, 2022, Nature Microbiology.

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

K. Murakami, V. Molodtsov, M. Z. Qayyum, 2021, bioRxiv.

Gene recognition by combination of several gene-finding programs

K. Murakami, T. Takagi, T. Takagi, 1998, Bioinform..

Repression and activation of promoter-bound RNA polymerase activity by Gal repressor.

K. Murakami, A. Ishihama, S. Adhya, 1997, Journal of molecular biology.

Role of the C-Terminal Domain of the Alpha Subunit of RNA Polymerase in LuxR-Dependent Transcriptional Activation of the lux Operon during Quorum Sensing

K. Murakami, A. Ishihama, A. Stevens, 2002, Journal of bacteriology.

Operon during Quorum Sensing lux of the LuxR-Dependent Transcriptional Activation Subunit of RNA Polymerase in Role of the C-Terminal Domain of the Alpha

K. Murakami, A. Ishihama, A. Stevens, 2002 .

Single-molecule imaging of RNA polymerase-DNA interactions in real time.

K. Murakami, T. Yanagida, Y. Harada, 1999, Biophysical journal.

Cra-Dependent Transcriptional Activation of theicd Gene of Escherichia coli

K. Murakami, A. Ishihama, D. Nègre, 1999, Journal of Bacteriology.

The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element.

M. Kimura, K. Murakami, A. Ishihama, 1997, Proceedings of the National Academy of Sciences of the United States of America.

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

Teruyoshi Hishiki, Katsuhiko Murakami, Yoshihiro Kawahara, 2007, Nucleic Acids Res..

A Database System for cDNA Expression Profile Using ESTs of Oligo-Capping Clones and UniGene

T. Ota, T. Nishikawa, T. Sugiyama, 2000 .

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

K. Murakami, V. Molodtsov, M. Z. Qayyum, 2021, The Journal of biological chemistry.

G-compass: a web-based comparative genome browser between human and other vertebrate genomes

Katsuhiko Murakami, Yoshihiro Kawahara, Yoshiharu Sato, 2009, Bioinform..

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees

Katsuhiko Murakami, Yoshihiro Kawahara, Yasuyuki Fujii, 2007, Nucleic Acids Res..

Activation of the catBCA promoter: probing the interaction of CatR and RNA polymerase through in vitro transcription

K. Murakami, A. Ishihama, A. Chakrabarty, 1997, Journal of bacteriology.

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

K. Murakami, T. Strick, J. R. Portman, 2022, Nucleic acids research.

Human ERG-2 protein is a phosphorylated DNA-binding protein--a distinct member of the ets family.

N. Bhat, K. Murakami, R. Fisher, 1993, Oncogene.

Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis

K. Murakami, R. Ghosh, P. Gollnick, 2016, Nucleic acids research.

Transcription Activation by the Bacteriophage Mu Mor Protein Requires the C-terminal Regions of Both α and σ70 Subunits of Escherichia coli RNA Polymerase*

K. Murakami, A. Ishihama, I. Artsimovitch, 1996, The Journal of Biological Chemistry.

Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression

Toshio Kojima, Yoshiyuki Sakaki, Y. Sakaki, 2004, BMC Genomics.

Mapping the promoter DNA sites proximal to conserved regions of sigma 70 in an Escherichia coli RNA polymerase-lacUV5 open promoter complex.

K. Murakami, N. Fujita, A. Ishihama, 1998, Biochemistry.

H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery

Takuya Habara, Jun-ichi Takeda, Chisato Yamasaki, 2012, Nucleic Acids Res..

Transcription factor recognition surface on the RNA polymerase alpha subunit is involved in contact with the DNA enhancer element.

K. Murakami, N. Fujita, A. Ishihama, 1996, The EMBO journal.

Analysis of citation network in PuMed Central papers

Katsuhiko Murakami, K. Murakami, 2016 .

Archaeal RNA polymerase subunits E and F are not required for transcription in vitro, but a Thermococcus kodakarensis mutant lacking subunit F is temperature‐sensitive

K. Murakami, T. Kanai, T. Imanaka, 2008, Molecular microbiology.

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

K. Murakami, A. Aravin, Sergei Ryazansky, 2022 .

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

K. Murakami, H. Showalter, S. Franzblau, 2022, ACS infectious diseases.

Novel Chemical Scaffolds for Inhibition of Rifamycin-Resistant RNA Polymerase Discovered from High-Throughput Screening.

K. Murakami, N. Scharf, G. Garcia, 2016, Journal of biomolecular screening.

The cyanobacterial principal σ factor region 1.1 is involved in DNA‐binding in the free form and in transcription activity as holoenzyme

K. Murakami, M. Hanaoka, M. Imashimizu, 2006, FEBS letters.

Crystal Structures of the ADP and ATP Bound Forms of the Bacillus Anti-σ Factor SpoIIAB in Complex with the Anti-anti-σ SpoIIAA

K. Murakami, S. Darst, E. Campbell, 2004 .

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

Fumikazu Konishi, Hammad Afzal, Gos Micklem, 2013, J. Biomed. Semant..

Identification of an UP element within the IHF binding site at the PL1-PL2 tandem promoter of bacteriophage lambda.

K. Murakami, A. Ishihama, A. Oppenheim, 1996, Journal of molecular biology.

Nucleic Acids and Molecular Biology

K. Murakami, M. Trakselis, Katsuhiko S. Murakami, 1988, Nucleic Acids and Molecular Biology.

Novel Chemical Scaffolds for Inhibition of Rifamycin-Resistant RNA Polymerase Discovered from High-Throughput Screening

K. Murakami, N. Scharf, G. Garcia, 2017, SLAS discovery : advancing life sciences R & D.