Deep trefoil knot implicated in RNA binding found in an archaebacterial protein

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2003-02, Vol.50 (2), p.177-183
• Main Authors: Zarembinski, Thomas I., Kim, Youngchang, Peterson, Kelly, Christendat, Dinesh, Dharamsi, Akil, Arrowsmith, Cheryl H., Edwards, Aled M., Joachimiak, Andrzej
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Archaeal Proteins - chemistry; Archaeal Proteins - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Crystallography, X-Ray; Dimerization; Models, Molecular; Molecular Sequence Data; Protein Structure, Secondary; Protein Structure, Tertiary; RNA - metabolism; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - metabolism
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.10311

( beta alpha ) sub(s) (TIM) barrel comprises one of the most abundant and versatile fold in nature. Although its structure is conserved, its primary sequence is highly divergent and gives rise to a plethora of distinct functions. Most structures deposited into the Protein Data Bank consist of the TIM barrel fold, and TIM barrel appears to be the most common fold in yeast. Nearly all TIM barrel proteins are enzymes, and so far, 15 distinct enzymatic functions have been assigned to TIM barrel containing proteins. (The exception, narbonin, has no known function.) Most commonly, their active sites are positioned within the beta alpha loops at the C-terminal end of the protein. TIM barrels are differentiated by auxiliary features such as location (and nature) of additional domains, identity of cofactor, number of ( beta alpha ) units, location of the barrel major axis, and are based on strand and shear number. In general, in all TIM barrels and most other protein folds the main-chain does not cross over (to form a knot), although protein topologies involving formation of a knot have been reported in proteins.