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Characterization of an SSB-dT25 complex: structural insights into the S-shaped ssDNA binding conformation. | LitMetric

Characterization of an SSB-dT25 complex: structural insights into the S-shaped ssDNA binding conformation.

RSC Adv

School of Biomedical Sciences, Chung Shan Medical University No. 110, Sec. 1, Chien-Kuo N. Rd. Taichung City Taiwan +886-4-24730022 ext. 11472.

Published: December 2019

AI Article Synopsis

Article Abstract

Single-stranded DNA (ssDNA)-binding proteins (SSBs) play an important role in all DNA-dependent cellular processes, such as DNA replication, recombination, repair, and replication restart. The N-terminal domain of SSBs forms an oligonucleotide/oligosaccharide-binding (OB) fold for ssDNA binding. The SSB-dC35 complex structure has revealed how an SSB (EcSSB) tetramer binds to 65-nucleotide (nt)-long ssDNA, namely, the (SSB) binding mode. Knowledge on whether the ssDNA-binding mode for EcSSB is typical for all SSBs or is bacterial strain and length dependent is limited. Here, we studied the ssDNA-binding properties of a SSB (PaSSB) and investigated its interaction mode through crystallographic analysis. The complex crystal structure containing a PaSSB tetramer with two ssDNA chains was solved at a resolution of 1.91 Å (PDB entry 6IRQ). Results revealed that each bound ssDNA dT25 adopts an S-shaped conformation. This binding mode, as shown by the complex structure of PaSSB, differs significantly from (SSB). ssDNA-binding contributions from aromatic residues in PaSSB, except the contribution of Trp54, were not significant. Using electrophoretic mobility shift analysis, we characterized the stoichiometry of PaSSB complexed with a series of ssDNA homopolymers. The minimal length of ssDNA required for PaSSB tetramer binding and the size of the ssDNA-binding site were 25 and 29 nt, respectively. These observations through structure-function analysis suggested that only two OB folds rather than four OB folds in PaSSB are enough for the formation of a stable complex with ssDNA. The PaSSB noninteracting OB folds proposed here may allow sliding reptation in a dynamic ssDNA binding process.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9076272PMC
http://dx.doi.org/10.1039/c9ra09406gDOI Listing

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