One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.
The eightfold (betaalpha) barrel structure, first observed in triose-phosphate isomerase, occurs ubiquitously in nature. It is nearly always an enzyme and most often involved in molecular or energy metabolism within the cell. In this review we bring together data on the sequence, structure and function of the proteins known to adopt this fold. We highlight the sequence and functional diversity in the 21 homologous superfamilies, which include 76 different sequence families. In many structures, the barrels are "mixed and matched" with other domains generating additional variety. Global and local structure-based alignments are used to explore the distribution of the associated functional residues on this common structural scaffold. Many of the substrates/co-factors include a phosphate moiety, which is usually but not always bound towards the C-terminal end of the sequence. Some, but not all, of these structures, exhibit a structurally conserved "phosphate binding motif". In contrast metal-ligating residues and catalytic residues are distributed along the sequence. However, we also found striking structural superposition of some of these residues. Lastly we consider the possible evolutionary relationships between these proteins, whose sequences are so diverse that even the most powerful approaches find few relationships, yet whose active sites all cluster at one end of the barrel. This extreme example of the "one fold-many functions" paradigm illustrates the difficulty of assigning function through a structural genomics approach for some folds.
Nagano
Nozomi
N
Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, Gower Street, UK. n.nagano@aist.go.jp
Orengo
Christine A
CA
Thornton
Janet M
JM
D019747:Aldose-Ketose Isomerases / Q000737:chemistry / Q000502:physiology; D000595:Amino Acid Sequence; D000619:Aminohydrolases / Q000737:chemistry / Q000502:physiology; D001665:Binding Sites; D004798:Enzymes / Q000737:chemistry* / Q000235:genetics / Q000502:physiology*; D019143:Evolution, Molecular; D008024:Ligands; D008969:Molecular Sequence Data; D010710:Phosphates / Q000378:metabolism; D010802:Phylogeny; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment
D004798:Enzymes; D008024:Ligands; D010710:Phosphates; C087227:imidazole glycerol phosphate synthase; D000619:Aminohydrolases; D019747:Aldose-Ketose Isomerases; C079656:Phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxiamide isomerase