From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold

Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4264-9. doi: 10.1073/pnas.0408056102. Epub 2005 Mar 14.

Abstract

The enzyme YkvM from Bacillus subtilis was identified previously along with three other enzymes (YkvJKL) in a bioinformatics search for enzymes involved in the biosynthesis of queuosine, a 7-deazaguanine modified nucleoside found in tRNA(GUN) of Bacteria and Eukarya. Genetic analysis of ykvJKLM mutants in Acinetobacter confirmed that each was essential for queuosine biosynthesis, and the genes were renamed queCDEF. QueF exhibits significant homology to the type I GTP cyclohydrolases characterized by FolE. Given that GTP is the precursor to queuosine and that a cyclohydrolase-like reaction was postulated as the initial step in queuosine biosynthesis, QueF was proposed to be the putative cyclohydrolase-like enzyme responsible for this reaction. We have cloned the queF genes from B. subtilis and Escherichia coli and characterized the recombinant enzymes. Contrary to the predictions based on sequence analysis, we discovered that the enzymes, in fact, catalyze a mechanistically unrelated reaction, the NADPH-dependent reduction of 7-cyano-7-deazaguanineto7-aminomethyl-7-deazaguanine, a late step in the biosynthesis of queuosine. We report here in vitro and in vivo studies that demonstrate this catalytic activity, as well as preliminary biochemical and bioinformatics analysis that provide insight into the structure of this family of enzymes.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acinetobacter / enzymology
  • Acinetobacter / genetics
  • Amino Acid Sequence
  • Bacillus subtilis / enzymology*
  • Bacillus subtilis / genetics
  • Base Sequence
  • DNA, Bacterial / genetics
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics
  • GTP Cyclohydrolase / chemistry*
  • GTP Cyclohydrolase / genetics
  • GTP Cyclohydrolase / metabolism*
  • Genes, Bacterial
  • Molecular Sequence Data
  • Nucleoside Q / biosynthesis
  • Oxidoreductases / chemistry*
  • Oxidoreductases / genetics
  • Oxidoreductases / metabolism*
  • Protein Folding
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Sequence Homology, Amino Acid

Substances

  • DNA, Bacterial
  • Recombinant Fusion Proteins
  • Nucleoside Q
  • Oxidoreductases
  • GTP Cyclohydrolase