Menu
Home
People
Places
Arts
History
Plants & Animals
Science
Life & Culture
Technology
Reference.org
Structural motif
open-in-new
<h2 id="in-nucleic-acids">In nucleic acids</h2> <p class="note">See also: <a href="/facts/Non-B_database/QFkwnCam">Non-B database</a></p> <p>Depending upon the sequence and other conditions, nucleic acids can form a variety of structural motifs which is thought to have biological significance. </p> <a href="/facts/Stem-loop/GysAzrX5">Stem-loop</a> Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA.<a class="footnote-ref" id="fnref:2" href="#fn:2"><sup>2</sup></a> The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures. <a href="/facts/Cruciform_DNA/79fXrNQa">Cruciform DNA</a> Cruciform DNA is a form of non-B DNA that requires at least a 6 <a href="/facts/Nucleotide/pQKEwlJI">nucleotide</a> sequence of <a href="/facts/Inverted_repeats/81kE3X3s">inverted repeats</a> to form a structure consisting of a stem, branch point and loop in the shape of a cruciform, stabilized by negative <a href="/facts/DNA_supercoiling/vFTgbyNT">DNA supercoiling</a>.<a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a> Two classes of cruciform DNA have been described; folded and unfolded. <a href="/facts/G-quadruplex/yFJyL0sy">G-quadruplex</a> <i>G-quadruplex</i> <a href="/facts/Nucleic_acid_secondary_structure/qXjlsFK5">secondary structures</a> (G4) are formed in nucleic acids by sequences that are rich in <a href="/facts/Guanine/hoTSpz0x">guanine</a>.<a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a> They are helical in shape and contain guanine tetrads that can form from one,<a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a> two<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> or four strands.<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> <a href="/facts/D-loop/4yt3q9n9">D-loop</a> A displacement loop or D-loop is a <a href="/facts/DNA/nB89Iauz">DNA</a> structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA.<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a> An <a href="/facts/R-loop/1vdPotfx">R-loop</a> is similar to a D-loop, but in this case the third strand is RNA rather than DNA.<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> The third strand has a <a href="/facts/Nucleobase/zj1Vl9Qh">base</a> sequence which is <a href="/facts/Complementarity_(molecular_biology)/WQfqGlBJ">complementary</a> to one of the main strands and <a href="/facts/Base_pair/xmPpPQ9W">pairs</a> with it, thus displacing the other complementary main strand in the region. Within that region the structure is thus a form of <a href="/facts/Triple-stranded_DNA/FKrSsBxe">triple-stranded DNA</a>. A diagram in the paper introducing the term illustrated the D-loop with a shape resembling a capital "D", where the displaced strand formed the loop of the "D".<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> <h2 id="in-proteins">In proteins</h2> <p>In proteins, a structural motif describes the connectivity between secondary structural elements. An individual motif usually consists of only a few elements, e.g., the 'helix-turn-helix' motif which has just three. Note that, while the <i>spatial sequence</i> of elements may be identical in all instances of a motif, they may be encoded in any order within the underlying <a href="/facts/Gene/e1swwPY6">gene</a>. In addition to secondary structural elements, protein structural motifs often include loops of variable length and unspecified structure. Structural motifs may also appear as <a href="/facts/Protein_tandem_repeats/1xxaUtyp">tandem repeats</a>. </p> <a href="/facts/Beta_hairpin/wHmw5Yfx">Beta hairpin</a> Extremely common. Two <a href="/facts/Antiparallel_(biochemistry)/IMsRKh5G">antiparallel</a> beta strands connected by a tight turn of a few amino acids between them. <a href="/facts/Beta_sheet/B6mwwR6H">Greek key</a> Four beta strands, three connected by hairpins, the fourth folded over the top. <a href="/facts/Omega_loop/Y7tgeI8L">Omega loop</a> A loop in which the residues that make up the beginning and end of the loop are very close together.<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a> <a href="/facts/Basic-helix-loop-helix/yqfuWejn">Helix-loop-helix</a> Consists of <a href="/facts/Alpha_helix/7CESPIYJ">alpha helices</a> bound by a looping stretch of amino acids. This motif is seen in transcription factors. <a href="/facts/Zinc_finger/dWrlw4t7">Zinc finger</a> Two beta strands with an alpha helix end folded over to bind a zinc <a href="/facts/Ion/3bePpDna">ion</a>. Important in DNA binding proteins. <a href="/facts/Helix-turn-helix/a2qHSHUL">Helix-turn-helix</a> Two α helices joined by a short strand of amino acids and found in many proteins that regulate gene expression.<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a> <a href="/facts/Nest_(protein_structural_motif)/hjckhbHu">Nest</a> Extremely common. Three consecutive amino acid residues form an anion-binding concavity.<a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a> <a href="/facts/Niche_(protein_structural_motif)/EhttCaMV">Niche</a> Extremely common. Three or four consecutive amino acid residues form a cation-binding feature.<a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/Sequence_motif/RtcoysBD">Sequence motif</a></li> <li><a href="/facts/Short_linear_motif/EqU80U6g">Short linear motif</a></li> <li><a href="/facts/Protein_tandem_repeats/1xxaUtyp">Protein tandem repeats</a></li></ul> <ul><li><a href="/facts/PROSITE/TcqJLVBc">PROSITE</a> <a href="http://www.expasy.org/prosite">Database of protein families and domains</a></li> <li><a href="/facts/Structural_Classification_of_Proteins/4uz6VcF7">SCOP</a> <a href="https://web.archive.org/web/20070911012207/http://scop.mrc-lmb.cam.ac.uk/scop/">Structural classification of Proteins</a></li> <li><a href="/facts/CATH/n5mBVu02">CATH</a> <a href="http://www.cathdb.info/">Class Architecture Topology Homology</a></li> <li><a href="/facts/Families_of_structurally_similar_proteins/mod5glph">FSSP</a> <a href="https://web.archive.org/web/20030925185235/http://www.bioinfo.biocenter.helsinki.fi:8080/dali/index.html">FSSP</a></li> <li>PASS2 <a href="https://web.archive.org/web/20060831195006/http://caps.ncbs.res.in/campass/pass.html">PASS2 - Protein Alignments as Structural Superfamilies</a></li> <li>SMoS <a href="http://caps.ncbs.res.in/SMoS">SMoS - Database of Structural Motifs of Superfamily</a> <a href="https://web.archive.org/web/20070126135233/http://caps.ncbs.res.in/SMoS/">Archived</a> 2007-01-26 at the <a href="/facts/Wayback_Machine/nmQ3a6JC">Wayback Machine</a></li> <li>S4 <a href="https://web.archive.org/web/20081121033341/http://www1.i2r.a-star.edu.sg/~azeyar/SuperSSE/">S4: Server for Super-Secondary Structure Motif Mining</a></li></ul> <h2 id="further-reading">Further reading</h2> <ul><li>Chiang YS, Gelfand TI, Kister AE, Gelfand IM (2007). "New classification of supersecondary structures of sandwich-like proteins uncovers strict patterns of strand assemblage". <i>Proteins</i>. 68 (4): 915–921. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1002%2Fprot.21473">10.1002/prot.21473</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/17557333">17557333</a>. <a href="/facts/S2CID_(identifier)/ldJsHa2Y">S2CID</a> <a href="https://api.semanticscholar.org/CorpusID:29904865">29904865</a>.</li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Johansson, M.U. (23 July 2012). "Defining and searching for structural motifs using DeepView/Swiss-PdbViewer". BMC Bioinformatics. 13 (173): 173. doi:10.1186/1471-2105-13-173. PMC 3436773. PMID 22823337. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436773" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436773</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Bolshoy, Alexander (2010). Genome Clustering: From Linguistic Models to Classification of Genetic Texts. Springer. p. 47. ISBN 9783642129513. Retrieved 24 March 2021. <a href="9783642129513" target="_blank">9783642129513</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Shlyakhtenko LS, Potaman VN, Sinden RR, Lyubchenko YL (July 1998). "Structure and dynamics of supercoil-stabilized DNA cruciforms". J. Mol. Biol. 280 (1): 61–72. CiteSeerX 10.1.1.555.4352. doi:10.1006/jmbi.1998.1855. PMID 9653031. <a href="/wiki/CiteSeerX_(identifier)" target="_blank">/wiki/CiteSeerX_(identifier)</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Routh ED, Creacy SD, Beerbower PE, Akman SA, Vaughn JP, Smaldino PJ (March 2017). "A G-quadruplex DNA-affinity Approach for Purification of Enzymaticacvly Active G4 Resolvase1". Journal of Visualized Experiments. 121 (121). doi:10.3791/55496. PMC 5409278. PMID 28362374. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5409278" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5409278</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Largy E, Mergny JL, Gabelica V (2016). "Chapter 7. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability". In Astrid S, Helmut S, Roland KO S (eds.). The Alkali Metal Ions: Their Role in Life (PDF). Metal Ions in Life Sciences. Vol. 16. Springer. pp. 203–258. doi:10.1007/978-3-319-21756-7_7. ISBN 978-3-319-21755-0. PMID 26860303. <a href="978-3-319-21755-0" target="_blank">978-3-319-21755-0</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Sundquist WI, Klug A (December 1989). "Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops". Nature. 342 (6251): 825–9. Bibcode:1989Natur.342..825S. doi:10.1038/342825a0. PMID 2601741. S2CID 4357161. <a href="/wiki/Bibcode_(identifier)" target="_blank">/wiki/Bibcode_(identifier)</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Sen D, Gilbert W (July 1988). "Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis". Nature. 334 (6180): 364–6. Bibcode:1988Natur.334..364S. doi:10.1038/334364a0. PMID 3393228. S2CID 4351855. <a href="/wiki/Bibcode_(identifier)" target="_blank">/wiki/Bibcode_(identifier)</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>DePamphilis, Melvin (2011). Genome Duplication. Garland Science, Taylor & Francis Group, LLC. p. 419. ISBN 9780415442060. Retrieved 24 March 2021. <a href="9780415442060" target="_blank">9780415442060</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Al-Hadid, Qais (July 1, 2016). "R-loop: an emerging regulator of chromatin dynamics". Acta Biochim Biophys Sin (Shanghai). 48 (7): 623–31. doi:10.1093/abbs/gmw052. PMC 6259673. PMID 27252122. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6259673" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6259673</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Kasamatsu, H.; Robberson, D. L.; Vinograd, J. (1971). "A novel closed-circular mitochondrial DNA with properties of a replicating intermediate". Proceedings of the National Academy of Sciences of the United States of America. 68 (9): 2252–2257. Bibcode:1971PNAS...68.2252K. doi:10.1073/pnas.68.9.2252. PMC 389395. PMID 5289384. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC389395" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC389395</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Hettiarachchy, Navam S (2012). Food Proteins and Peptides: Chemistry, Functionality, Interactions, and Commercialization. CRC Press Taylor & Francis Group. p. 16. ISBN 9781420093421. Retrieved 24 March 2021. <a href="9781420093421" target="_blank">9781420093421</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Dubey, R C (2014). Advanced Biotechnology. S Chand Publishing. p. 505. ISBN 978-8121942904. Retrieved 24 March 2021. <a href="978-8121942904" target="_blank">978-8121942904</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>Milner-White, E. James (September 26, 2011). "Functional Capabilities of the Earliest Peptides and the Emergence of Life". Genes. 2 (4): 674. doi:10.3390/genes2040671. PMC 3927598. PMID 24710286. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927598" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927598</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>Milner-White, E. James (September 26, 2011). "Functional Capabilities of the Earliest Peptides and the Emergence of Life". Genes. 2 (4): 678. doi:10.3390/genes2040671. PMC 3927598. PMID 24710286. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927598" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927598</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> </ol>