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OB-fold
open-in-new
<h2 id="structure">Structure</h2> <p>The OB-fold consists of a five-stranded <a href="/facts/Beta_sheet/B6mwwR6H">β-sheet</a> coiled to form a closed <a href="/facts/Beta_barrel/8UMBqHQh">β-barrel</a>, capped by an <a href="/facts/Alpha_helix/7CESPIYJ">α-helix</a> 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.<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a><a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> </p> <h3>Structural determinants</h3> <p>OB-fold domains have several key structural determinants. These common features arise from physical principles governing <a href="/facts/Protein_structure/BptnTs9X">protein structure</a> rather than from <a href="/facts/Sequence_homology/mCIVStrA">sequence homology</a>.<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a><a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> </p> <ul><li>β-sheet structure:</li></ul> <p>The closed β-sheet has specific parameters that determine <a href="/facts/Shape/nww0x85d">geometrical features</a> like mean radius and average angle between strand directions and barrel axis. </p> <ul><li>β-bulges:</li></ul> <p>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. </p> <ul><li>Interior residue packing:</li></ul> <p>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. </p> <ul><li>β-barrel deformation:</li></ul> <p>Many β-barrels are similarly flattened, with an elliptical cross-section. </p> <ul><li>Barrel-helix interface:</li></ul> <p>A cavity on the barrel axis is filled by a large <a href="/facts/Hydrophobe/Ifya0CXQ">hydrophobic</a> residue from the helix. </p> <ul><li>Binding site location:</li></ul> <p>In some proteins, the <a href="/facts/Binding_site/gd9r9Rw7">binding sites</a> 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. </p> <h2 id="function">Function</h2> <p>OB-folds are versatile <a href="/facts/Binding_domain/4q2qSJdR">binding domains</a> that can interact with <a href="/facts/Single-stranded_DNA/nB89Iauz">single-stranded DNA</a> (ssDNA), <a href="/facts/Double-stranded_DNA/nB89Iauz">double-stranded DNA</a> (dsDNA), <a href="/facts/RNA/HxPeNfNj">RNA</a>, <a href="/facts/Protein/Jxmagu3E">proteins</a>, <a href="/facts/Phospholipid/u6GhNCF5">phospholipids</a> and <a href="/facts/Oligosaccharide/5to180o3">oligosaccharides</a>. In genome guardian proteins, OB-folds play crucial roles in DNA binding and recognition, <a href="/facts/Protein%25E2%2580%2593protein_interaction/etvm9Wmg">protein-protein interactions</a> and <a href="/facts/Catalysis/LPBS7TQC">catalytic</a> functions in multi-subunit complexes.<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> </p> <h2 id="examples-of-proteins-containing-this-domain">Examples of proteins containing this domain</h2> <ul><li><a href="/facts/Single-stranded_binding_protein/ErU6f0kb">Single-stranded DNA binding protein</a> (SSB)</li> <li><a href="/facts/Replication_protein_A/dN7d9RC6">Replication Protein A</a> (RPA)</li> <li>RecG helicase</li> <li><a href="/facts/RuvABC/NQeT90fK">RuvA</a> (part of the Holliday junction branch migration complex)</li> <li><a href="/facts/Minichromosome_maintenance/MbJFI5Nd">Minichromosome maintenance</a> (MCM) proteins</li> <li>DNA ligase III</li> <li>RecO (recombination mediator)</li></ul> <h2 id="relationship-to-sh3-domains">Relationship to SH3 domains</h2> <p>OB-folds are structurally similar to <a href="/facts/SH3_domain/aFNwnKe8">Src homology 3 (SH3) domains</a>, 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.<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a> </p> <h2 id="evolution-and-distribution">Evolution and distribution</h2> <p>The OB-fold may represent a stable folding motif that appeared early in <a href="/facts/Protein_evolution/lmMbqfzH">protein evolution</a>, with its wide occurrence due to its adaptability to different functions and sequences.<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a> 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 <a href="/facts/Oligomer/v7oDY8zu">oligomerisation states</a> 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 <a href="/facts/Catalysis/LPBS7TQC">catalytic</a> functions to multi-subunit complexes, expanding its utility beyond just binding. Its structural similarity to SH3 domains allows OB-folds to participate in <a href="/facts/Protein%25E2%2580%2593protein_interaction/etvm9Wmg">protein-protein interactions</a>, enabling regulation and complex formation.<a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a> </p> <h2 id="external-links">External links</h2> <ul><li><a href="https://www.ebi.ac.uk/interpro/entry/InterPro/IPR012340/">InterPro: Nucleic acid-binding, OB-fold (IPR012340)</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Murzin AG (March 1993). "OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences". The EMBO Journal. 12 (3): 861–867. doi:10.1002/j.1460-2075.1993.tb05726.x. PMC 413284. PMID 8458342. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC413284" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC413284</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Amir M, Alam A, Ishrat R, Alajmi MF, Hussain A, Rehman MT, et al. (September 2020). "A Systems View of the Genome Guardians: Mapping the Signaling Circuitry Underlying Oligonucleotide/Oligosaccharide-Binding Fold Proteins". Omics. 24 (9): 518–530. doi:10.1089/omi.2020.0072. PMID 32780668. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Yang Z, Costanzo M, Golde DW, Kolesnick RN (September 1993). "Tumor necrosis factor activation of the sphingomyelin pathway signals nuclear factor kappa B translocation in intact HL-60 cells". The Journal of Biological Chemistry. 268 (27): 20520–20523. doi:10.1016/s0021-9258(20)80756-x. PMC 8376408. PMID 8376408. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8376408" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8376408</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Murzin AG (March 1993). "OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences". The EMBO Journal. 12 (3): 861–867. doi:10.1002/j.1460-2075.1993.tb05726.x. PMC 413284. PMID 8458342. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC413284" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC413284</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Theobald DL, Mitton-Fry RM, Wuttke DS (2003). "Nucleic acid recognition by OB-fold proteins". Annual Review of Biophysics and Biomolecular Structure. 32: 115–133. doi:10.1146/annurev.biophys.32.110601.142506. PMC 1564333. PMID 12598368. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1564333" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1564333</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Murzin AG (March 1993). "OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences". The EMBO Journal. 12 (3): 861–867. doi:10.1002/j.1460-2075.1993.tb05726.x. PMC 413284. PMID 8458342. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC413284" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC413284</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Bianco PR (2022). "OB-fold Families of Genome Guardians: A Universal Theme Constructed From the Small β-barrel Building Block". Frontiers in Molecular Biosciences. 9: 784451. doi:10.3389/fmolb.2022.784451. PMC 8881015. PMID 35223988. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8881015" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8881015</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Murzin AG (March 1993). "OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences". The EMBO Journal. 12 (3): 861–867. doi:10.1002/j.1460-2075.1993.tb05726.x. PMC 413284. PMID 8458342. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC413284" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC413284</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Theobald DL, Mitton-Fry RM, Wuttke DS (2003). "Nucleic acid recognition by OB-fold proteins". Annual Review of Biophysics and Biomolecular Structure. 32: 115–133. doi:10.1146/annurev.biophys.32.110601.142506. PMC 1564333. PMID 12598368. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1564333" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1564333</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Flynn RL, Zou L (August 2010). "Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians". Critical Reviews in Biochemistry and Molecular Biology. 45 (4): 266–275. doi:10.3109/10409238.2010.488216. PMC 2906097. PMID 20515430. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906097" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906097</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Bianco PR (2022). "OB-fold Families of Genome Guardians: A Universal Theme Constructed From the Small β-barrel Building Block". Frontiers in Molecular Biosciences. 9: 784451. doi:10.3389/fmolb.2022.784451. PMC 8881015. PMID 35223988. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8881015" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8881015</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Murzin AG (March 1993). "OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences". The EMBO Journal. 12 (3): 861–867. doi:10.1002/j.1460-2075.1993.tb05726.x. PMC 413284. PMID 8458342. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC413284" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC413284</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>Bianco PR (2022). "OB-fold Families of Genome Guardians: A Universal Theme Constructed From the Small β-barrel Building Block". Frontiers in Molecular Biosciences. 9: 784451. doi:10.3389/fmolb.2022.784451. PMC 8881015. PMID 35223988. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8881015" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8881015</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> </ol>