title: OB-fold: growing bigger with functional consistency.
abstract: It was predicted that the folding space for various protein sequences is restricted and a maximum of 1000 protein folds could be expected. Although, there were about 648 folds identified, general functional features of individual folds is not thoroughly studied. We selected OB-fold, which is supposed to be an oligonucleotide and oligosaccharide binding fold to study the general functional features. OB-fold is a small beta-barrel fold formed from 5 strands connected by modulating loops. We observed consistently 2 or 3 loops on the same face of barrel acting as clamps to bind to their ligands. Depending on the ligand, which could be a single or double stranded DNA/RNA or an oligosaccharide, and their conformational properties the loops change in length and sequence to accommodate various ligands. Different classes of OB-folded proteins were analyzed and found that the functional features are retained in spite of negligible sequence homology among various proteins studied.
authors.affiliation: Institute of Microbial Technology, Sector 39-A, Chandigarh 160 036, India.
authors.forename: Vishal
authors.initials: V
authors.lastname: Agrawal
authors.forename: K V Radha
authors.initials: KV
authors.lastname: Kishan
mesh_terms: D000818:Animals; D001427:Bacterial Toxins / Q000737:chemistry / Q000378:metabolism; D016208:Databases, Factual; D006801:Humans; D008958:Models, Molecular; D009841:Oligonucleotides / Q000378:metabolism*; D009844:Oligosaccharides / Q000378:metabolism*; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012313:RNA / Q000378:metabolism; D012269:Ribosomal Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D001427:Bacterial Toxins; D009841:Oligonucleotides; D009844:Oligosaccharides; D010446:Peptide Fragments; D012269:Ribosomal Proteins; D012313:RNA