title: Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins.
abstract: BACKGROUND
  Enzymes are complex catalytic machines, which perform sequences of elementary chemical transformations resulting in biochemical function. The building blocks of enzymes, elementary functional loops (EFLs), possess distinct functional signatures and provide catalytic and binding amino acids to the enzyme's active sites. The goal of this work is to obtain primordial prototypes of EFLs that existed before the formation of enzymatic domains and served as their building blocks.
  
  
  RESULTS
  We developed a computational strategy for reconstructing ancient prototypes of EFLs based on the comparison of sequence segments on the proteomic scale, which goes beyond detection of conserved functional motifs in homologous proteins. We illustrate the procedure by a CxxC-containing prototype with a very basic and ancient elementary function of metal/metal-containing cofactor binding and redox activity. Acquiring the prototypes of EFLs is necessary for revealing how the original set of protein folds with enzymatic functions emerged in predomain evolution.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
  
  
  BACKGROUND
  igor.berezovsky@uni.no.
authors: Computational Biology Unit, Uni Research, University of Bergen, N-5008 Bergen, Norway.
authors: Alexander
authors: A
authors: Goncearenco
authors: Igor N
authors: IN
authors: Berezovsky
mesh_terms: D019295:Computational Biology; D003545:Cysteine / Q000737:chemistry; D004798:Enzymes / Q000737:chemistry; D019143:Evolution, Molecular; D008667:Metalloproteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein
chemical_list: D004798:Enzymes; D008667:Metalloproteins; D003545:Cysteine