OB-fold Families of Genome Guardians: A Universal Theme Constructed From the Small β-barrel Building Block

Piero R Bianco

doi:10.3389/fmolb.2022.784451

Abstract

The maintenance of genome stability requires the coordinated actions of multiple proteins and protein complexes, that are collectively known as genome guardians. Within this broadly defined family is a subset of proteins that contain oligonucleotide/oligosaccharide-binding folds (OB-fold). While OB-folds are widely associated with binding to single-stranded DNA this view is no longer an accurate depiction of how these domains are utilized. Instead, the core of the OB-fold is modified and adapted to facilitate binding to a variety of DNA substrates (both single- and double-stranded), phospholipids, and proteins, as well as enabling catalytic function to a multi-subunit complex. The flexibility accompanied by distinctive oligomerization states and quaternary structures enables OB-fold genome guardians to maintain the integrity of the genome via a myriad of complex and dynamic, protein-protein; protein-DNA, and protein-lipid interactions in both prokaryotes and eukaryotes.

Highlights

The small β-barrel (SBB) family of proteins is a large and ubiquitous family with diverse metabolic functions (Youkharibache et al, 2019)
The binding mechanism employed in the linker/oligosaccharidebinding folds (OB-fold) model to regulate the single-strand DNA binding (SSB) interactome is similar to that used by Src homology 3 (SH3) domains to bind PXXP motifs to mediate target protein function (Bianco et al, 2017; Saksela and Permi, 2012; Yu et al, 1994)
The conformational change in the protein associated with binding of SSB to singlestranded DNA (ssDNA) makes linkers available for interactome partner binding which facilitates these proteins being loaded onto the DNA, their functions regulated, and, in some cases, this is accompanied by SSB dissociation (Bell et al, 2015; Sun et al, 2015; Bianco et al, 2017; Nigam et al, 2018; Ding et al, 2020; Hwang et al, 2020; Wang et al, 2020)

Summary

Introduction

The small β-barrel (SBB) family of proteins is a large and ubiquitous family with diverse metabolic functions (Youkharibache et al, 2019). The variation in OB-folds suggests that proteins containing these domains may bind to DNA substrates in distinct ways to effect different reaction outcomes while maintaining genome integrity.

Results

Conclusion