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2020

Crystal structure of the complex of the interaction domains of Escherichia coli DnaB helicase and DnaC helicase loader: Structural basis implying a distortion-accumulation mechanism for the DnaB ring opening caused by DnaC binding

Nagata, K., Okada, A., Ohtsuka, J., Ohkuri, T., Akama, Y., Sakiyama, Y., Miyazaki, E., Horita, S., Katayama, T., Ueda, T. & Tanokura, M., Jan 1 2020, In : Journal of biochemistry. 167, 1, p. 1-14 14 p.

Research output: Contribution to journalArticle

Open Access
2019

A novel mode of DnaA-DnaA interaction promotes ADP dissociation for reactivation of replication initiation activity

Sugiyama, R., Kasho, K., Miyoshi, K., Ozaki, S., Kagawa, W., Kurumizaka, H. & Katayama, T., Dec 2 2019, In : Nucleic acids research. 47, 21, p. 11209-11224 16 p.

Research output: Contribution to journalArticle

Open Access
Open Access
2 Citations (Scopus)

Specific basic patch-dependent multimerization of Saccharomyces cerevisiae ORC on single-stranded DNA promotes ATP hydrolysis

Kawakami, H., Muraoka, R., Ohashi, E., Kawabata, K., Kanamoto, S., Chichibu, T., Tsurimoto, T. & Katayama, T., Sep 1 2019, In : Genes to Cells. 24, 9, p. 608-618 11 p.

Research output: Contribution to journalArticle

2018

The DnaA AAA+ Domain His136 residue directs DnaB replicative helicase to the unwound region of the replication origin, oriC

Sakiyama, Y., Nishimura, M., Hayashi, C., Akama, Y., Ozaki, S. & Katayama, T., Aug 31 2018, In : Frontiers in Microbiology. 9, AUG, 2017.

Research output: Contribution to journalArticle

3 Citations (Scopus)
2017

Cooperative DnaA binding to the negatively supercoiled datA locus stimulates DnaA-ATP hydrolysis

Kasho, K., Tanaka, H., Sakai, R. & Katayama, T., Jan 27 2017, In : Journal of Biological Chemistry. 292, 4, p. 1251-1266 16 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)

Exponential propagation of large circular DNA by reconstitution of a chromosome-replication cycle

Su’etsugu, M., Takada, H., Katayama, T. & Tsujimoto, H., Jan 1 2017, In : Nucleic acids research. 45, 20, p. 11525-11534 10 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Expression of a Vibrio parahaemolyticus toxin in Escherichia coli results in chromosomal DNA degradation

Zhang, J., Taniguchi, S., Ito, H., Iiyama, K., Hino, M., Katayama, T. & Kimura, M., Jan 1 2017, In : Bioscience, Biotechnology and Biochemistry. 81, 10, p. 1937-1940 4 p.

Research output: Contribution to journalArticle

Regulatory dynamics in the ternary DnaA complex for initiation of chromosomal replication in Escherichia coli

Sakiyama, Y., Kasho, K., Noguchi, Y., Kawakami, H. & Katayama, T., Dec 1 2017, In : Nucleic acids research. 45, 21, p. 12354-12373 20 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)
2016

Chromosomal location of the DnaA-reactivating sequence DARS2 is important to regulate timely initiation of DNA replication in Escherichia coli

Inoue, Y., Tanaka, H., Kasho, K., Fujimitsu, K., Oshima, T. & Katayama, T., Sep 1 2016, In : Genes to Cells. 21, 9, p. 1015-1023 9 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Long inverted repeat transiently stalls DNA replication by forming hairpin structures on both leading and lagging strands

Lai, P. J., Lim, C. T., Le, H. P., Katayama, T., Leach, D. R. F., Furukohri, A. & Maki, H., Feb 1 2016, In : Genes to Cells. 21, 2, p. 136-145 10 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights

Shimizu, M., Noguchi, Y., Sakiyama, Y., Kawakami, H., Katayama, T. & Takada, S., Dec 13 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 50, p. E8021-E8030

Research output: Contribution to journalArticle

15 Citations (Scopus)
1 Citation (Scopus)

Site-Specific Turn-On Fluorescent Labeling of DNA-Interacting Protein Using Oligodeoxynucleotides That Modify Lysines to Produce 5,6-Dimethoxy 3-Methyleneisoindolin-1-one

Gatanaga, C., Yang, B., Inadomi, Y., Usui, K., Ota, C., Katayama, T., Suemune, H. & Aso, M., Aug 19 2016, In : ACS Chemical Biology. 11, 8, p. 2216-2221 6 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)
7 Citations (Scopus)
2015

Basic and aromatic residues in the C-terminal domain of PriC are involved in ssDNA and SSB binding

Aramaki, T., Abe, Y., Furutani, K., Katayama, T. & Ueda, T., Jan 1 2015, In : Journal of Biochemistry. 157, 6, p. 529-537 9 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Bioconjugation of Oligodeoxynucleotides Carrying 1,4-Dicarbonyl Groups via Reductive Amination with Lysine Residues

Yang, B., Jinnouchi, A., Usui, K., Katayama, T., Fujii, M., Suemune, H. & Aso, M., Aug 19 2015, In : Bioconjugate Chemistry. 26, 8, p. 1830-1838 9 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Functional analysis of CedA based on its structure: Residues important in binding of DNA and RNA polymerase and in the cell division regulation

Abe, Y., Fujisaki, N., Miyoshi, T., Watanabe, N., Katayama, T. & Ueda, T., May 13 2015, In : Journal of biochemistry. 159, 2, p. 217-223 7 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Short CCG repeat in huntingtin gene is an obstacle for replicative DNA polymerases, potentially hampering progression of replication fork

Le, H. P., Masuda, Y., Tsurimoto, T., Maki, S., Katayama, T., Furukohri, A. & Maki, H., Oct 2015, In : Genes to Cells. 20, 10, p. 817-833 17 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Specific binding of eukaryotic ORC to DNA replication origins depends on highly conserved basic residues

Kawakami, H., Ohashi, E., Kanamoto, S., Tsurimoto, T. & Katayama, T., Oct 12 2015, In : Scientific reports. 5, 14929.

Research output: Contribution to journalArticle

9 Citations (Scopus)

The Arg fingers of key DnaA protomers are oriented inward within the replication origin oriC and stimulate DnaA subcomplexes in the initiation complex

Noguchi, Y., Sakiyama, Y., Kawakami, H. & Katayama, T., Aug 14 2015, In : Journal of Biological Chemistry. 290, 33, p. 20295-20312 18 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)
2014

DNA polymerase IV mediates efficient and quick recovery of replication forks stalled at N2-dG adducts

Ikeda, M., Furukohri, A., Philippin, G., Loechler, E., Akiyama, M. T., Katayama, T., Fuchs, R. P. & Maki, H., 2014, In : Nucleic acids research. 42, 13, p. 8461-8472 12 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Involvement of histidine in complex formation of PriB and single-stranded DNA

Fujiyama, S., Abe, Y., Takenawa, T., Aramaki, T., Shioi, S., Katayama, T. & Ueda, T., Feb 1 2014, In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1844, 2, p. 299-307 9 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Structure and mechanism of the primosome protein DnaT-functional structures for homotrimerization, dissociation of ssDNA from the PriB·ssDNA complex, and formation of the DnaT·ssDNA complex

Fujiyama, S., Abe, Y., Tani, J., Urabe, M., Sato, K., Aramaki, T., Katayama, T. & Ueda, T., Dec 2014, In : FEBS Journal. 281, 23, p. 5356-5370 15 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Timely binding of IHF and Fis to DARS2 regulates ATP-DnaA production and replication initiation

Kasho, K., Fujimitsu, K., Matoba, T., Oshima, T. & Katayama, T., Dec 1 2014, In : Nucleic acids research. 42, 21, p. 13134-13149 16 p.

Research output: Contribution to journalArticle

31 Citations (Scopus)
2013

A replicase clamp-binding dynamin-like protein promotes colocalization of nascent DNA strands and equipartitioning of chromosomes in E.coli

Ozaki, S., Matsuda, Y., Keyamura, K., Kawakami, H., Noguchi, Y., Kasho, K., Nagata, K., Masuda, T., Sakiyama, Y. & Katayama, T., May 12 2013, In : Cell Reports. 4, 5, p. 985-995 11 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Cooperative working of bacterial chromosome replication proteins generated by a reconstituted protein expression system

Fujiwara, K., Katayama, T. & Nomura, S. I. M., Aug 1 2013, In : Nucleic acids research. 41, 14, p. 7176-7183 8 p.

Research output: Contribution to journalArticle

30 Citations (Scopus)
57 Citations (Scopus)

Domain separation and characterization of PriC, a replication restart primosome factor in Escherichia coli

Aramaki, T., Abe, Y., Ohkuri, T., Mishima, T., Yamashita, S., Katayama, T. & Ueda, T., Sep 1 2013, In : Genes to Cells. 18, 9, p. 723-732 10 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Regulating DNA replication in bacteria

Skarstad, K. & Katayama, T., Apr 1 2013, In : Cold Spring Harbor Perspectives in Biology. 5, 4, p. 1-17 17 p.

Research output: Contribution to journalArticle

108 Citations (Scopus)

Solution structure of the N-terminal domain of a replication restart primosome factor, PriC, in Escherichia coli

Aramaki, T., Abe, Y., Katayama, T. & Ueda, T., Sep 1 2013, In : Protein Science. 22, 9, p. 1279-1286 8 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

The DnaA N-terminal domain interacts with Hda to facilitate replicase clamp-mediated inactivation of DnaA

Su'etsugu, M., Harada, Y., Keyamura, K., Matsunaga, C., Kasho, K., Abe, Y., Ueda, T. & Katayama, T., Dec 1 2013, In : Environmental Microbiology. 15, 12, p. 3183-3195 13 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)
2012

Differentiation of the DnaA-oriC subcomplex for DNA unwinding in a replication initiation complex

Ozaki, S., Noguchi, Y., Hayashi, Y., Miyazaki, E. & Katayama, T., Oct 26 2012, In : Journal of Biological Chemistry. 287, 44, p. 37458-37471 14 p.

Research output: Contribution to journalArticle

35 Citations (Scopus)

Highly organized DnaA-oriC complexes recruit the single-stranded DNA for replication initiation

Ozaki, S. & Katayama, T., Feb 1 2012, In : Nucleic acids research. 40, 4, p. 1648-1665 18 p.

Research output: Contribution to journalArticle

65 Citations (Scopus)

Stable nucleotide binding to DnaA requires a specific glutamic acid residue within the AAA+ box II motif

Ozaki, S., Noguchi, Y., Nishimura, M. & Katayama, T., Aug 1 2012, In : Journal of structural biology. 179, 2, p. 242-250 9 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)
2011
18 Citations (Scopus)

DNA replication defects in a mutant deficient in the thioredoxin homolog YbbN

Le, H. T., Gautier, V., Kthiri, F., Kohiyama, M., Katayama, T. & Richarme, G., Feb 4 2011, In : Biochemical and Biophysical Research Communications. 405, 1, p. 52-57 6 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Suppressors of DnaAATP imposed overinitiation in Escherichia coli

Charbon, G., Riber, L., Cohen, M., Skovgaard, O., Fujimitsu, K., Katayama, T. & Løbner-Olesen, A., Feb 1 2011, In : Molecular Microbiology. 79, 4, p. 914-928 15 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)
2010
21 Citations (Scopus)
2009

DiaA dynamics are coupled with changes in initial origin complexes leading to helicase loading

Keyamura, K., Abe, Y., Higashi, M., Ueda, T. & Katayama, T., Sep 11 2009, In : Journal of Biological Chemistry. 284, 37, p. 25038-25050 13 p.

Research output: Contribution to journalArticle

56 Citations (Scopus)

Loss of Hda activity stimulates replication initiation from I-box, but not R4 mutant origins in Escherichia coli

Riber, L., Fujimitsu, K., Katayama, T. & Løbner-Olesen, A., Jan 1 2009, In : Molecular Microbiology. 71, 1, p. 107-122 16 p.

Research output: Contribution to journalArticle

34 Citations (Scopus)

Specific genomic sequences of E. coli promote replicational initiation by directly reactivating ADP-DnaA

Fujimitsu, K., Senriuchi, T. & Katayama, T., May 15 2009, In : Genes and Development. 23, 10, p. 1221-1233 13 p.

Research output: Contribution to journalArticle

82 Citations (Scopus)
2008

A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin

Ozaki, S., Kawakami, H., Nakamura, K., Fujikawa, N., Kagawa, W., Park, S. Y., Yokoyama, S., Kurumizaka, H. & Katayama, T., Mar 28 2008, In : Journal of Biological Chemistry. 283, 13, p. 8351-8362 12 p.

Research output: Contribution to journalArticle

86 Citations (Scopus)

Hda monomerization by ADP binding promotes replicase clamp-mediated DnaA-ATP hydrolysis

Su'etsugu, M., Nakamura, K., Keyamura, K., Kudo, Y. & Katayama, T., Dec 26 2008, In : Journal of Biological Chemistry. 283, 52, p. 36118-36131 14 p.

Research output: Contribution to journalArticle

33 Citations (Scopus)

Modes of overinitiation, dnaA gene expression, and inhibition of cell division in a novel cold-sensitive hda mutant of Escherichia coli

Fujimitsu, K., Su'etsugu, M., Yamaguchi, Y., Mazda, K., Fu, N., Kawakami, H. & Katayama, T., Aug 1 2008, In : Journal of bacteriology. 190, 15, p. 5368-5381 14 p.

Research output: Contribution to journalArticle

44 Citations (Scopus)

Roles for the AAA+ motifs of DnaA in the initiation of DNA replication

Katayama, T., Feb 2008, In : Biochemical Society Transactions. 36, 1, p. 78-82 5 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)
2007

Assignment of 1H, 13C and 15N resonances of N-terminal domain of DnaA protein

Abe, Y., Watanabe, N., Yoshida, Y., Ebata, F., Katayama, T. & Ueda, T., Jul 1 2007, In : Biomolecular NMR Assignments. 1, 1, p. 57-59 3 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Structure and function of DnaA N-terminal domains: Specific sites and mechanisms in inter-DnaA interaction and in DnaB helicase loading on oriC

Abe, Y., Jo, T., Matsuda, Y., Matsunaga, C., Katayama, T. & Ueda, T., Jun 15 2007, In : Journal of Biological Chemistry. 282, 24, p. 17816-17827 12 p.

Research output: Contribution to journalArticle

76 Citations (Scopus)

The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP-DnaA-specific initiation complexes

Keyamura, K., Fujikawa, N., Ishida, T., Ozaki, S., Su'etsugu, M., Fujimitsu, K., Kagawa, W., Yokoyama, S., Kurumizaka, H. & Katayama, T., Aug 15 2007, In : Genes and Development. 21, 16, p. 2083-2099 17 p.

Research output: Contribution to journalArticle

92 Citations (Scopus)
2006

An isolated Hda-clamp complex is functional in the regulatory inactivation of DnaA and DNA replication

Kawakami, H., Su'etsugu, M. & Katayama, T., Oct 1 2006, In : Journal of structural biology. 156, 1, p. 220-229 10 p.

Research output: Contribution to journalArticle

23 Citations (Scopus)