A deep trefoil knot in a Thermus thermophilus RNA methyltransferase domain (PDB ID 1IPA). The knotted C-terminus of the protein is shown in blue.

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 RNA binding proteins in archaea^[1] and in methyltransferase proteins^[2] and tRNA modification proteins^[3] in the bacterium Thermus thermophilus. Knotted proteins have not yet been reported in eukaryotes. Thermus thermophilus is a gram negative eubacterium used in a range of biotechnological applications, including as a model organism for genetic manipulation. ... Ribonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers. ... The C-terminal end refers to the extremity of a protein or polypeptide terminated by an amino acid with a free carboxyl group (COOH). ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... In biochemistry, the tertiary structure of a protein is its overall shape. ... A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ... Categories: Stub | Knot theory ... Ribonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers. ... Phyla / Classes Phylum Crenarchaeota Phylum Euryarchaeota     Halobacteria     Methanobacteria     Methanococci     Methanopyri     Archaeoglobi     Thermoplasmata     Thermococci Phylum Korarchaeota Phylum Nanoarchaeota Archaea (; from Greek αρχαία, old ones; singular Archaeum, Archaean, or Archaeon), also called Archaebacteria (), is a major division of living organisms. ... Transfer RNA (abbreviated tRNA) is a small RNA chain (74-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. ... Phyla/Divisions Actinobacteria Aquificae Bacteroidetes/Chlorobi Chlamydiae/Verrucomicrobia Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Nitrospirae Omnibacteria Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Bacteria (singular, bacterium) are a major group of living organisms. ... Thermus thermophilus is a gram negative eubacterium used in a range of biotechnological applications, including as a model organism for genetic manipulation. ... Kingdoms Animalia - Animals Fungi Plantae - Plants Protista An eukaryote (yoo-KAR-ee-ot) is an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus or nuclei. ...

In many cases the trefoil knot is part of the active 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^[4]. 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^[5]. The active site of an enzyme is the binding site where catalysis occurs. ... Ribbon diagram of the enzyme TIM, surrounded by the space-filling model of the protein. ... Protein folding is the process by which a protein assumes its characteristic functional shape or tertiary structure, also known as the native state. ... Kinetics refers to two different areas of science: Chemical kinetics studies reaction rates. ... Sucrose, or common table sugar, is composed of glucose and fructose. ... Binomial name Haemophilus influenzae (Lehmann & Neumann 1896) Winslow 1917 Haemophilus influenzae, formerly called Pfeiffers bacillus or Bacillus influenzae, is a non-motile Gram-negative coccobacillus first described in 1892 by Dr. Richard Pfeiffer during an influenza pandemic. ... L-Proline is one of the twenty proteinogenic units which are used in living organisms as the building blocks of proteins. ... The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. ... Protein structure prediction is one of the most significant technologies pursued by computational structural biology and theoretical chemistry. ...

External links

• SCOP alpha/beta knot fold
• CATH alpha/beta knot topology

References

1. ↑  Zarembinski TI, Kim Y, Peterson K, Christendat D, Dharamsi A, Arrowsmith CH, Edwards AM, Joachimiak A. (2003). Deep trefoil knot implicated in RNA binding found in an archaebacterial protein. Proteins 50(2):177-83.
2. ↑  Nureki O, Shirouzu M, Hashimoto K, Ishitani R, Terada T, Tamakoshi M, Oshima T, Chijimatsu M, Takio K, Vassylyev DG, Shibata T, Inoue Y, Kuramitsu S, Yokoyama S. (2002). An enzyme with a deep trefoil knot for the active-site architecture. Acta Crystallogr D Biol Crystallogr 58(Pt 7):1129-37.
3. ↑  Nureki O, Watanabe K, Fukai S, Ishii R, Endo Y, Hori H, Yokoyama S. (2004). Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure 12(4):593-602.
4. ↑  Mallam AL, Jackson SE. (2006). Probing nature's knots: the folding pathway of a knotted homodimeric protein. J Mol Biol 359(5):1420-36.
5. ↑  Khatib F, Weirauch MT, Rohl CA. (2006). Rapid knot detection and application to protein structure prediction. Bioinformatics 22(14):e252-9.