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

Masahiro Shimizu, Yasunori Noguchi, Yukari Sakiyama, Hironori Kawakami, Tsutomu Katayama, Shoji Takada

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.

Original languageEnglish
Pages (from-to)E8021-E8030
JournalProceedings of the National Academy of Sciences of the United States of America
Volume113
Issue number50
DOIs
Publication statusPublished - Dec 13 2016

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Bacterial DNA
Structural Models
DNA Replication
DNA
DnaB Helicases
Escherichia coli Proteins
Computer Simulation
Adenosine Triphosphatases
Proteins

All Science Journal Classification (ASJC) codes

  • General

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Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights. / Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 113, No. 50, 13.12.2016, p. E8021-E8030.

Research output: Contribution to journalArticle

Shimizu, Masahiro ; Noguchi, Yasunori ; Sakiyama, Yukari ; Kawakami, Hironori ; Katayama, Tsutomu ; Takada, Shoji. / Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights. In: Proceedings of the National Academy of Sciences of the United States of America. 2016 ; Vol. 113, No. 50. pp. E8021-E8030.
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