OB-fold
OB-fold
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OB-fold

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OB-fold

In molecular biology, the OB-fold (oligonucleotide/oligosaccharide-binding fold) is a small protein structural motif observed in different proteins that bind oligonucleotides or oligosaccharides. It was originally identified in 1993 in four unrelated proteins: staphylococcal nuclease, anticodon binding domain of aspartyl-tRNA synthetase, and the B-subunits of heat-labile enterotoxin and verotoxin-1. Since then it has been found in multiple proteins many of which are involved in genome stability. This fold is often described as a Greek key motif.

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.

OB-fold domains have several key structural determinants. These common features arise from physical principles governing protein structure rather than from sequence homology.

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

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.

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.

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

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

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