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Structural and functional characterization of TraI from pKM101 reveals basis for DNA processing
Open accessPublished version of a preprint
Abstract
Type 4 secretion systems are large and versatile protein machineries that facilitate the spread of antibiotic resistance and other virulence factors via horizontal gene transfer. Conjugative type 4 secretion systems depend on relaxases to process the DNA in preparation for transport. TraI from the well-studied conjugative plasmid pKM101 is one such relaxase. Here, we report the crystal structure of the trans-esterase domain of TraI in complex with its substrate oriT DNA, highlighting the conserved DNA-binding mechanism of conjugative relaxases. In addition, we present an apo structure of the trans-esterase domain of TraI that includes most of the flexible thumb region. This allows us for the first time to visualize the large conformational change of the thumb subdomain upon DNA binding. We also characterize the DNA binding, nicking, and religation activity of the trans-esterase domain, helicase domain, and full-length TraI. Unlike previous indications in the literature, our results reveal that the TraI trans-esterase domain from pKM101 behaves in a conserved manner with its homologs from the R388 and F plasmids.
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Metadata
- Authors
- Breidenstein, A., ter Beek, J., & Berntsson, R. P.-A.
- Affiliations
- Umeå University (SE)
- Corresponding author
- ter Beek, Josy
- Berntsson, Ronnie P-A
- Venue
- Life Science Alliance
- Publisher
- Life Science Alliance, LLC
- Published
- 2023-01-20
- Volume
- 6
- Issue
- 4
- Pages
- e202201775
- ISSN
- 2575-1077 (ISSN-L)
- PMC
- PMC9868005
- OpenAlex
- W4317548989
- Cited by
- 3
- References
- 1
- Citations by year
- 2025: 1 · 2024: 2
- FWCI
- 0.50
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Life Science Alliance (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DiVA at Umeå University (Umeå University) (submittedVersion, cc-by)
- DORA PSI (Paul Scherrer Institute) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Swedish Research Council (2018-07152, 2016-03599)
- Swedish Governmental Agency for Innovation Systems (2018-04969)
- Formas (2019-02496)
- Kempestiftelserna (SMK-1762, SMK-1869)
- Knut and Alice Wallenberg Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- DNA binding mechanism, crystal structure, horizontal gene transfer, antibiotic resistance plasmids, F plasmid
- MeSH terms
- Type IV Secretion Systems, DNA, Esterases, Plasmids, Escherichia coli Proteins
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