AI Article Synopsis

  • The study focuses on the role of the DnaT protein in the primosome of Escherichia coli, indicating its importance in restarting DNA replication at damaged sites.
  • Researchers identified two domains in DnaT and highlighted a critical 24-residue region necessary for its trimerization.
  • They also determined the structure of the C-terminal domain using NMR spectroscopy and suggested that specific residues facilitate ssDNA binding and help dissociate it from protein complexes, providing insights into DnaT's mechanism in DNA repair processes.

Article Abstract

Unlabelled: In Escherichia coli, the primosome plays an essential role in replication restart after dissociation of replisomes at the damaged replication fork. As well as PriA and PriB, DnaT, an ssDNA-binding protein, is a key member of the primosome. In this study, limited proteolysis indicated that E. coli DnaT was composed of two domains, consistent with the results of recent studies using Klebsiella pneumonia DnaT. We also found that a specific 24-residue region (Phe42-Asp66) in the N-terminal domain (1-88) was crucial for DnaT trimerization. Moreover, we determined the structure of the DnaT C-terminal domain (89-179) by NMR spectroscopy. This domain included three α-helices and a long flexible C-terminal tail, similar to the C-terminal subdomain of the AAA+ ATPase family. The neighboring histidines, His136 and His137, at a position corresponding to the AAA+ sensor II motif, were suggested to form an ssDNA-binding site. Furthermore, we found that the acidic linker between the two domains had an activity for dissociating ssDNA from the PriB·ssDNA complexes in a manner supported by the conserved acidic residues Asp70 and Glu76. Thus, these findings provide a novel structural basis for understanding the mechanism of DnaT in exposure of ssDNA and reloading of the replicative helicase at the stalled replication fork.

Database: The coordinates used for the ensemble of NMR structures have been deposited in the Protein Data Bank under accession code 2ru8. The NMR data have been deposited in the BioMagResBank (www.bmrb.wisc.edu) under accession number 11549.

Download full-text PDF

Source
http://dx.doi.org/10.1111/febs.13080DOI Listing

Publication Analysis

Top Keywords

ssdna prib·ssdna
8
dnat
6
structure mechanism
4
mechanism primosome
4
primosome protein
4
protein dnat-functional
4
dnat-functional structures
4
structures homotrimerization
4
homotrimerization dissociation
4
dissociation ssdna
4

Similar Publications

Smart shape-memory DNA hydrogels, which can respond to various types of external stimuli and undergo macroscopic shape deformations, have shown great potential in various applications. By constructing free-standing films, the deformation and response properties of these hydrogels can be further enhanced, and visualized deformation can be achieved. However, DNA hydrogels that can exhibit rapid and high-degree shape deformations, such as the inverse shape deformations, are still lacking.

View Article and Find Full Text PDF

Variability in HIV-1 transmitted/founder virus susceptibility to combined APOBEC3F and APOBEC3G host restriction.

J Virol

December 2024

Department of Biochemistry, Microbiology, and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.

Several APOBEC3 enzymes restrict HIV-1 by deaminating cytosine to form uracil in single-stranded proviral (-)DNA. However, HIV-1 Vif counteracts their activity by inducing their proteasomal degradation. This counteraction by Vif is incomplete, as evidenced by footprints of APOBEC3-mediated mutations within integrated proviral genomes of people living with HIV-1.

View Article and Find Full Text PDF

Micron-scale colloidal particles with short-ranged attractions, e.g., colloids functionalized with single-stranded DNA oligomers, have emerged as a powerful platform for studying colloidal self-assembly phenomena with the long-term goal of identifying routes for metamaterial fabrication.

View Article and Find Full Text PDF

Photo-Cross-linked DNA Structures Greatly Improves Their Serum Nuclease Resistances and Gene Knock-In Efficiencies.

Small Methods

December 2024

Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.

The stabilization and structural integrity of DNA architectures remain significant challenges in their biomedical applications, particularly when inserting functional units into the genome using long single-stranded DNA (lssDNA). To address these challenges, a site-specific photo-cross-linking method is employed. Single-stranded oligonucleotides, containing one or two photosensitive cyanovinylcarbazole nucleoside (K) molecules, are precisely incorporated and cross-linked at the specific sites of ssDNA through base-pairing, followed by rapid UV irradiation at 365 nm.

View Article and Find Full Text PDF

Internal State of Vesicles Affects Higher Order State of Vesicle Assembly and Interaction.

ACS Omega

December 2024

Cellular Computational and Biology Department, CIBIO, Laboratory for Artificial Biology, University of Trento, Via Sommarive 9, Povo 38123, Italy.

Dynamic soft matter systems composed of functionalized vesicles and liposomes are typically produced and then manipulated through external means, including the addition of exogenous molecules. In biology, natural cells possess greater autonomy, as their internal states are continuously updated, enabling them to effect higher order properties of the system. Therefore, a conceptual and technical gap exists between the natural and artificial systems.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!

A PHP Error was encountered

Severity: Notice

Message: fwrite(): Write of 34 bytes failed with errno=28 No space left on device

Filename: drivers/Session_files_driver.php

Line Number: 272

Backtrace:

A PHP Error was encountered

Severity: Warning

Message: session_write_close(): Failed to write session data using user defined save handler. (session.save_path: /var/lib/php/sessions)

Filename: Unknown

Line Number: 0

Backtrace: