title: The structures and physicochemical properties of organic cofactors in biocatalysis.
abstract: Many crucial biochemical reactions in the cell require not only enzymes for catalysis but also organic cofactors or metal ions. Here, we analyse the physicochemical properties, chemical structures and functions of organic cofactors. Based on a thorough analysis of the literature complemented by our quantitative characterisation and classification, we found that most of these molecules are constructed from nucleotide and amino-acid-type building blocks, as well as some recurring cofactor-specific chemical scaffolds. We show that, as expected, organic cofactors are on average significantly more polar and slightly larger than other metabolites in the cell, yet they cover the full spectrum of physicochemical properties found in the metabolome. Furthermore, we have identified intrinsic groupings among the cofactors, based on their molecular properties, structures and functions, that represent a new way of considering cofactors. Although some classes of cofactors, as defined by their physicochemical properties, exhibit clear structural communalities, cofactors with similar structures can have diverse functional and physicochemical profiles. Finally, we show that the molecular functions of the cofactors not only may duplicate reactions performed by inorganic metal cofactors and amino acids, the cell's other catalytic tools, but also provide novel chemistries for catalysis.
authors.affiliation: EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. julia.fischer@ebi.ac.uk
authors.forename: Julia D
authors.initials: JD
authors.lastname: Fischer
authors.forename: Gemma L
authors.initials: GL
authors.lastname: Holliday
authors.forename: Syed A
authors.initials: SA
authors.lastname: Rahman
authors.forename: Janet M
authors.initials: JM
authors.lastname: Thornton
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D002384:Catalysis; D055598:Chemical Phenomena; D003067:Coenzymes / Q000737:chemistry* / Q000145:classification / Q000378:metabolism*; D016208:Databases, Factual; D008670:Metals / Q000378:metabolism; D015394:Molecular Structure; D025341:Principal Component Analysis
chemical_list: D000596:Amino Acids; D003067:Coenzymes; D008670:Metals