Structural characterization of a hypothetical protein: a potential agent involved in trimethylamine metabolism in Catenulispora acidiphila

J Struct Funct Genomics. 2014 Mar;15(1):33-40. doi: 10.1007/s10969-014-9176-z. Epub 2014 Feb 22.

Abstract

Catenulispora acidiphila is a newly identified lineage of actinomycetes that produces antimicrobial activities and represents a promising source of novel antibiotics and secondary metabolites. Among the discovered protein coding genes, 68 % were assigned a putative function, while the remaining 32 % are genes encoding "hypothetical" proteins. Caci_0382 is one of the "hypothetical" proteins that has very few homologs. Sequence analysis shows that the protein belongs to the NTF2-like protein family. The structure of Caci_0382 demonstrates that it shares the same fold and has a similar active site as limonene-1,2-epoxide hydrolase, which suggests that it may have a related function. Using a fluorescence thermal shift assay, we identified stabilizing compounds that suggest potential natural ligands of Caci_0382. Using this information, we determined the crystal structure in complex with trimethylamine to provide a better understanding of the function of this uncharacterized protein.

Publication types

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

MeSH terms

  • Actinomycetales / enzymology*
  • Amino Acid Sequence
  • Bacterial Proteins / genetics
  • Bacterial Proteins / ultrastructure*
  • Catalytic Domain
  • Cloning, Molecular
  • Epoxide Hydrolases / genetics
  • Epoxide Hydrolases / ultrastructure*
  • Ligands
  • Methylamines / metabolism*
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation

Substances

  • Bacterial Proteins
  • Ligands
  • Methylamines
  • Epoxide Hydrolases
  • limonene-1,2-epoxide hydrolase
  • trimethylamine