Mimicking enzyme evolution by generating new (betaalpha)8-barrels from (betaalpha)4-half-barrels

Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16448-53. doi: 10.1073/pnas.0405832101. Epub 2004 Nov 11.

Abstract

Gene duplication and fusion events that multiply and link functional protein domains are crucial mechanisms of enzyme evolution. The analysis of amino acid sequences and three-dimensional structures suggested that the (betaalpha)8-barrel, which is the most frequent fold among enzymes, has evolved by the duplication, fusion, and mixing of (betaalpha)4-half-barrel domains. Here, we mimicked this evolutionary strategy by generating in vitro (betaalpha)8-barrels from (betaalpha)4-half-barrels that were deduced from the enzymes imidazole glycerol phosphate synthase (HisF) and N'[(5'-phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide isomerase (HisA). To this end, the gene for the C-terminal (betaalpha)4-half-barrel (HisF-C) of HisF was duplicated and fused in tandem to yield HisF-CC, which is more stable than HisF-C. In the next step, by optimizing side-chain interactions within the center of the beta-barrel of HisF-CC, the monomeric and compact (betaalpha)8-barrel protein HisF-C*C was generated. Moreover, the genes for the N- and C-terminal (betaalpha)4-half-barrels of HisF and HisA were fused crosswise to yield the chimeric proteins HisFA and HisAF. Whereas HisFA contains native secondary structure elements but adopts ill-defined association states, the (betaalpha)8-barrel HisAF is a stable and compact monomer that reversibly unfolds with high cooperativity. The results obtained suggest a previously undescribed dimension for the diversification of enzymatic activities: new (betaalpha)8-barrels with novel functions might have evolved by the exchange of (betaalpha)4-half-barrel domains with distinct functional properties.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aldose-Ketose Isomerases / chemistry*
  • Aldose-Ketose Isomerases / genetics
  • Aldose-Ketose Isomerases / metabolism
  • Aminohydrolases / chemistry*
  • Aminohydrolases / genetics
  • Aminohydrolases / metabolism
  • Base Sequence
  • Cloning, Molecular
  • DNA, Bacterial / genetics
  • Evolution, Molecular
  • Gene Duplication
  • Genes, Bacterial
  • Models, Molecular
  • Protein Structure, Secondary
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Thermotoga maritima / enzymology
  • Thermotoga maritima / genetics

Substances

  • DNA, Bacterial
  • Recombinant Proteins
  • imidazole glycerol phosphate synthase
  • Aminohydrolases
  • Aldose-Ketose Isomerases
  • Phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxiamide isomerase