Trefoil knot fold

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" ref|Nureki1 and proteinsref|Nureki2, in archaearef|Zarembinski 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 isomerizationref|Mallam. 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 proteinsref|Khatib. Currently, there is a web server pKNOTref|Lai available to detect knots in proteins as well as to provide information on knotted proteins in Protein Data Bank.

External links

* [http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.df.A.html SCOP alpha/beta knot fold]
* [http://www.cathdb.info/cgi-bin/cath/GotoCath.pl?cath=3.40.1280 CATH alpha/beta knot topology]
* [http://pknot.life.nctu.edu.tw/ pKNOT the web server to detect knots in proteins]

References

# 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.
# 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.
# 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.
# Leulliot N, Bohnsack MT, Graille M, Tollervey D, Van Tilbeurgh H.(2008). The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases. "Nucleic Acids Res" 36(2):629-39.
# Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM. (2007). Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. "BMC Bioinformatics". 8:73.
# Mallam AL, Jackson SE. (2006). Probing nature's knots: the folding pathway of a knotted homodimeric protein. "J Mol Biol" 359(5):1420-36.
# Khatib F, Weirauch MT, Rohl CA. (2006). Rapid knot detection and application to protein structure prediction. "Bioinformatics" 22(14):e252-9.
# Lai YL, Yen SC, Yu SH, Hwang JK (2007). pKNOT: the protein KNOT web server. "Nucleic Acids Research" 35:W420-424.