OB-fold

The OB-fold consists of a five-stranded β-sheet coiled to form a closed β-barrel, capped by an α-helix located at one end and a binding cleft at the other. The α-helix packs against the bottom layer of residues, roughly perpendicular to the barrel axis. The β-sheet structure protrudes beyond this layer and packs around the sides of the helix. The binding specificities of each OB-fold depend on the different length, sequence, and conformation of the loops connecting the β-strands.{{cite journal | vauthors = Murzin AG | title = OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences | journal = The EMBO Journal | volume = 12 | issue = 3 | pages = 861–867 | date = March 1993 | doi = 10.1002/j.1460-2075.1993.tb05726.x | pmid = 8458342 | pmc = 413284 }}{{cite journal | vauthors = Bianco PR | title = OB-fold Families of Genome Guardians: A Universal Theme Constructed From the Small β-barrel Building Block | journal = Frontiers in Molecular Biosciences | volume = 9 | pages = 784451 | date = 2022 | doi = 10.3389/fmolb.2022.784451 | doi-access = free | pmid = 35223988 | pmc = 8881015 }}

OB-fold domains have several key structural determinants. These common features arise from physical principles governing protein structure rather than from sequence homology.{{cite journal | vauthors = Theobald DL, Mitton-Fry RM, Wuttke DS | title = Nucleic acid recognition by OB-fold proteins | journal = Annual Review of Biophysics and Biomolecular Structure | volume = 32 | pages = 115–133 | date = 2003 | pmid = 12598368 | pmc = 1564333 | doi = 10.1146/annurev.biophys.32.110601.142506 }}

• β-sheet structure:

The closed β-sheet has specific parameters that determine geometrical features like mean radius and average angle between strand directions and barrel axis.

• β-bulges:

Most structures have a common β-bulge in the first strand. β-bulges provide small increases in barrel radius and required coiling of β-strands.

• Interior residue packing:

The interior of the closed β-sheet has a regular three-layer structure of residues, with each β-strand contributing one residue to each layer.

• β-barrel deformation:

Many β-barrels are similarly flattened, with an elliptical cross-section.

• Barrel-helix interface:

A cavity on the barrel axis is filled by a large hydrophobic residue from the helix.

• Binding site location:

In some proteins, the binding sites are located on the side surface of the β-barrel where three loops come together, in such a way they are partially wrapped by the binding partner. In others, the binding cleft at the side of the barrel opposite to the helix functions as binding site.

OB-folds are versatile binding domains that can interact with single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), RNA, proteins, phospholipids and oligosaccharides. In genome guardian proteins, OB-folds play crucial roles in DNA binding and recognition, protein-protein interactions and catalytic functions in multi-subunit complexes.{{cite journal | vauthors = Flynn RL, Zou L | title = Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians | journal = Critical Reviews in Biochemistry and Molecular Biology | volume = 45 | issue = 4 | pages = 266–275 | date = August 2010 | doi = 10.3109/10409238.2010.488216 | pmid = 20515430 | pmc = 2906097 }}

• Single-stranded DNA binding protein (SSB)
• Replication Protein A (RPA)
• RecG helicase
• RuvA (part of the Holliday junction branch migration complex)
• Minichromosome maintenance (MCM) proteins
• DNA ligase III
• RecO (recombination mediator)

OB-folds are structurally similar to Src homology 3 (SH3) domains, with their β-strands superimposing with less than 2 Å difference. This structural similarity is important for understanding OB-fold function and regulation, as SH3 domains bind to PXXP-containing ligands in a pocket similar to the ssDNA binding pocket of many OB-folds.

The OB-fold may represent a stable folding motif that appeared early in protein evolution, with its wide occurrence due to its adaptability to different functions and sequences. OB-fold proteins present great versatility, which likely contributed to the development and widespread adoption of the fold in genome guardian proteins. They can adopt various oligomerisation states and quaternary structures, allowing for complex and dynamic interactions. The OB-fold has flexibility in binding to a variety of substrates through variations in loop sizes, compositions, and insertions, showing a modular nature. In some cases, it can provide catalytic functions to multi-subunit complexes, expanding its utility beyond just binding. Its structural similarity to SH3 domains allows OB-folds to participate in protein-protein interactions, enabling regulation and complex formation.

{{Reflist}}

• [https://www.ebi.ac.uk/interpro/entry/InterPro/IPR012340/ InterPro: Nucleic acid-binding, OB-fold (IPR012340)]

Category:Protein domains

Category:Protein folds

Category:Protein superfamilies