| dbo:abstract |
The trefoil knot fold is a protein fold in which the protein backbone is twisted into a trefoil knot shape. "Shallow" knots in which the tail of the polypeptide chain only passes through a loop by a few residues are uncommon, but "deep" knots in which many residues are passed through the loop are extremely rare. Deep trefoil knots have been found in the SPOUT superfamily. including methyltransferase proteins involved in posttranscriptional RNA modification in all three Domains of Life, including bacterium Thermus thermophilus and proteins, in archaea and in eukaryota. In many cases the trefoil knot is part of the active site or a ligand-binding site and is critical to the activity of the enzyme in which it appears. Before the discovery of the first knotted protein, it was believed that the process of protein folding could not efficiently produce deep knots in protein backbones. Studies of the folding kinetics of a dimeric protein from Haemophilus influenzae have revealed that the folding of trefoil knot proteins may depend on proline isomerization. Computational algorithms have been developed to identify knotted protein structures, both to canvas the Protein Data Bank for previously undetected natural knots and to identify knots in protein structure predictions, where they are unlikely to accurately reproduce the native-state structure due to the rarity of knots in known proteins. Currently, there is a web server pKNOT available to detect knots in proteins as well as to provide information on knotted proteins in the Protein Data Bank.Knottins are small, diverse and stable proteins with important drug design potential. They can be classified in 30 families which cover a wide range of sequences (1621 sequenced), three-dimensional structures (155 solved) and functions (> 10). Inter knottin similarity lies mainly between 20% and 40% sequence identity and 1.5 to 4 A backbone deviations although they all share a tightly knotted disulfide core. This important variability is likely to arise from the highly diverse loops which connect the successive knotted cysteines. The prediction of structural models for all knottin sequences would open new directions for the analysis of interaction sites and to provide a better understanding of the structural and functional organization of proteins sharing this scaffold. (en) 三葉結び目フォールド（さんようむすびめフォールド、Trefoil knot fold）はタンパク質フォールドの1つで、全体がねじれて三葉結び目型を作る構造をしている。多くは緩い結び目で、ポリペプチド鎖のテールがループを数残基通るに過ぎないが、多くの残基がループを通過するきつい結び目のものも極まれにある。きつい結び目のものは古細菌のRNA結合タンパク質、またサーマス・サーモフィルスのメチルトランスフェラーゼや転移RNA修飾タンパク質で見られる。真核生物では三葉結び目フォールドのタンパク質は見つかっていない。 多くの場合この構造は活性部位にあり、酵素の活性にとって重要な働きをしている。この構造が発見されるまでは、タンパク質フォールドでは結び目のある形は効率よく作り出せないと信じられていた。インフルエンザ菌のタンパク質のフォールディングの力学的な研究によって、三葉結び目フォールドの形成はプロリンの異性化によって起こることが明らかとなった。結び目構造の同定のためにコンピュータを用いたアルゴリズムが開発され、蛋白質構造データバンクやタンパク質構造予測を進めた。 (ja) |
| dbo:symbol |
Trefoil |
| dbo:thumbnail |
wiki-commons:Special:FilePath/Trefoil-knot-1ipa.png?width=300 |
| dbo:wikiPageExternalLink |
https://web.archive.org/web/20070312154618/http:/www.cathdb.info/cgi-bin/cath/GotoCath.pl%3Fcath=3.40.1280 http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.df.A.html https://web.archive.org/web/20110824133833/http:/pknot.life.nctu.edu.tw/ |
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6402531 (xsd:integer) |
| dbo:wikiPageLength |
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| dbo:wikiPageRevisionID |
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| dbo:wikiPageWikiLink |
dbr:Proline dbr:Protein_structure_prediction dbr:Trefoil_factor_2 dbr:Gastric_acid dbr:Trefoil_factor_3 dbr:Enzyme dbr:Archaea dbr:Haemophilus_influenzae dbr:Protein_Data_Bank dbr:Protein_superfamily dbr:Bacterium dbr:Active_site dbr:Eukaryota dbr:Alpha-glucosidase dbc:Protein_folds dbc:Protein_tandem_repeats dbr:Acid_alpha-glucosidase dbr:Knotted_protein dbr:Protein_dimer dbr:Protein_domain dbr:Protein_folding dbr:Protein dbr:RNA dbc:Protein_domains dbr:Thermus_thermophilus dbr:Tertiary_structure dbr:Trefoil_knot dbr:Zona_pellucida dbr:Xenopus_laevis dbr:Methyltransferase dbr:ZP4 dbr:Secretion dbr:Maltase-glucoamylase dbr:Motility dbr:Mucin dbr:Peptide_bond dbr:Sucrase-isomaltase dbr:Trefoil_factor_1 dbr:Stomach_mucosa dbr:TFF1 dbr:TFF2 dbr:TFF3 dbr:File:Trefoil-knot-1ipa.png |
| dbp:caption |
Structure of pancreatic spasmolytic polypeptide. (en) |
| dbp:cdd |
cd00111 (en) |
| dbp:interpro |
IPR000519 (en) |
| dbp:name |
Trefoil domain (en) |
| dbp:pdb |
A:31-72 2:31-72 :30-71 B:30-71 A:28-70 B:28-70 :28-70 (en) |
| dbp:pfam |
PF00088 (en) |
| dbp:prosite |
PDOC00024 (en) |
| dbp:scop |
1 (xsd:integer) |
| dbp:smart |
SM00018 (en) |
| dbp:symbol |
Trefoil (en) |
| dbp:wikiPageUsesTemplate |
dbt:EC_number dbt:InterPro_content dbt:Ref dbt:Reflist dbt:Protein_tandem_repeats dbt:PDB3 dbt:Protein_tertiary_structure dbt:Pfam_box |
| dct:subject |
dbc:Protein_folds dbc:Protein_tandem_repeats dbc:Protein_domains |
| gold:hypernym |
dbr:Protein |
| rdf:type |
owl:Thing dbo:Biomolecule wikidata:Q206229 wikidata:Q8054 yago:Abstraction100002137 yago:AngularShape113864763 yago:Attribute100024264 yago:Fold113907415 dbo:Protein yago:Shape100027807 yago:WikicatProteinFolds |
| rdfs:comment |
三葉結び目フォールド（さんようむすびめフォールド、Trefoil knot fold）はタンパク質フォールドの1つで、全体がねじれて三葉結び目型を作る構造をしている。多くは緩い結び目で、ポリペプチド鎖のテールがループを数残基通るに過ぎないが、多くの残基がループを通過するきつい結び目のものも極まれにある。きつい結び目のものは古細菌のRNA結合タンパク質、またサーマス・サーモフィルスのメチルトランスフェラーゼや転移RNA修飾タンパク質で見られる。真核生物では三葉結び目フォールドのタンパク質は見つかっていない。 多くの場合この構造は活性部位にあり、酵素の活性にとって重要な働きをしている。この構造が発見されるまでは、タンパク質フォールドでは結び目のある形は効率よく作り出せないと信じられていた。インフルエンザ菌のタンパク質のフォールディングの力学的な研究によって、三葉結び目フォールドの形成はプロリンの異性化によって起こることが明らかとなった。結び目構造の同定のためにコンピュータを用いたアルゴリズムが開発され、蛋白質構造データバンクやタンパク質構造予測を進めた。 (ja) The trefoil knot fold is a protein fold in which the protein backbone is twisted into a trefoil knot shape. "Shallow" knots in which the tail of the polypeptide chain only passes through a loop by a few residues are uncommon, but "deep" knots in which many residues are passed through the loop are extremely rare. Deep trefoil knots have been found in the SPOUT superfamily. including methyltransferase proteins involved in posttranscriptional RNA modification in all three Domains of Life, including bacterium Thermus thermophilus and proteins, in archaea and in eukaryota. (en) |
| rdfs:label |
三葉結び目フォールド (ja) Trefoil knot fold (en) |
| owl:sameAs |
freebase:Trefoil knot fold yago-res:Trefoil knot fold wikidata:Trefoil knot fold dbpedia-ja:Trefoil knot fold dbpedia-sh:Trefoil knot fold dbpedia-sr:Trefoil knot fold https://global.dbpedia.org/id/4wSWq |
| prov:wasDerivedFrom |
wikipedia-en:Trefoil_knot_fold?oldid=1052099670&ns=0 |
| foaf:depiction |
wiki-commons:Special:FilePath/PDB_1psp_EBI.jpg wiki-commons:Special:FilePath/Trefoil-knot-1ipa.png |
| foaf:isPrimaryTopicOf |
wikipedia-en:Trefoil_knot_fold |
| is dbo:wikiPageDisambiguates of |
dbr:Trefoil_(disambiguation) |
| is dbo:wikiPageRedirects of |
dbr:Trefoil_domain |
| is dbo:wikiPageWikiLink of |
dbr:Conotoxin dbr:Folding@home dbr:Trefoil_(disambiguation) dbr:Trefoil_domain |
| is foaf:primaryTopic of |
wikipedia-en:Trefoil_knot_fold |
