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Cited by 3Bacterial Genetics and BiotechnologyEnzyme Structure and FunctionDNA Repair Mechanisms

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Distinct quaternary states, intermediates, and autoinhibition during loading of the DnaB-replicative helicase by the phage λP helicase loader

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Shatarupa, Abhipsa, Brown, Dhanjai, Olinares, Paul Dominic B, Chase, Jillian, Isiorho, Eta, Chait, Brian T, Jeruzalmi, David·2025·Nucleic Acids Research
DOI 10.1093/nar/gkaf1139PMC PMC12661323

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Abstract

Replicative helicases need loader proteins to assemble at DNA replication origins. Multiple copies of the bacteriophage λP (P) loader bind and load the Escherichia coli DnaB (B) replicative helicase onto single-stranded (ss) DNA from the replication origin. We find that the E. coli DnaB•λP complex exists in two forms: B6P5 and B6P6. In the 2.66 Å cryo-EM structure of B6P5, five λP loader copies form a crown-like shape that tightly grips DnaB. In this complex, the closed, planar DnaB is reconfigured into an open spiral with a large enough breach to allow ssDNA to enter an internal chamber. Transition to the open spiral involves λP-induced changes to the Docking Helix (DH)–Linker Helix (LH) interface. Unexpectedly, one λP chain in B6P5 is positioned across the breach. The disposition of this λP chain implies a complex pathway for entry of a replication-origin-derived ssDNA “bubble” ssDNA into the B6P5 complex. We propose that the B6P6 complex is an early intermediate in helicase activation in which neither DnaB nor λP has reached its final form. In this complex, DnaB adopts a partially open, ajar planar configuration. λP in B6P6 interacts more loosely with DnaB. The ssDNA- and ATP-binding sites in both complexes are not correctly configured for binding or hydrolysis. Our findings detail the distinct conformations of B6P6 and B6P5, allowing us to propose a structural model for the transition from an ajar planar to an open spiral configuration in the helicase loading pathway.

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Metadata

Authors
Shatarupa, A., Brown, D., Olinares, P. D. B., Chase, J., Isiorho, E., Chait, B. T., & Jeruzalmi, D.
Affiliations
  • The Graduate Center, CUNY (US)
  • Rockefeller University (US)
  • City University of New York (US)
Corresponding author
Jeruzalmi, David
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2025-11-26
Volume
53
Issue
22
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkaf1139
PMC
PMC12661323
OpenAlex
W4416815575
Cited by
3
References
2
Citations by year
2026: 2 · 2025: 1
FWCI
1.75
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion)
Funders
  • National Science Foundation (DJ: MCB 1818255, MCB #1818255)
  • National Institutes of Health (DJ: GM08416, BTC: P41 GM109824, OD019994, P41 GM103314, RR029300, P30 GM124165)
  • Department of Education (JC: PA200A150068)
  • Simons Foundation (SF349247)
  • National Institute of General Medical Sciences (GM103310)
  • Agouron Institute (F00316)
  • HEI (S10OD021527)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
Keywords
DnaB helicase, helicase loading, origin of replication, autoinhibition, Escherichia coli, cryo-EM structure

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