The solution structure of the N-terminal domain of riboflavin synthase

J Mol Biol. 2001 Jun 15;309(4):949-60. doi: 10.1006/jmbi.2001.4683.


The structure of the amino-terminal domain of Escherichia coli riboflavin synthase (RiSy) has been determined by NMR spectroscopy with riboflavin as a bound ligand. RiSy is functional as a 75 kDa homotrimer, each subunit of which consists of two domains which share very similar sequences and structures. The N-terminal domain (RiSy-N; 97 residues) forms a 20 kDa homodimer in solution which binds riboflavin with high affinity. The structure features a six-stranded antiparallel beta-barrel with a Greek-key fold, both ends of which are closed by an alpha-helix. One riboflavin molecule is bound per monomer in a site at one end of the barrel which is comprised of elements of both monomers. The structure and ligand binding are similar to that of the FAD binding domains of ferrodoxin reductase family proteins. The structure provides insights into the structure of the whole enzyme, the organisation of the functional trimer and the mechanism of riboflavin synthesis. C48 from the N-terminal domain is identified as the free cysteine implicated in a nucleophilic role in the synthesis mechanism, while H102 from the C-terminal domains is also likely to play a key role. Both are invariant in all known riboflavin synthase sequences.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Dimerization
  • Escherichia coli / enzymology*
  • Ligands
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Protein Subunits
  • Riboflavin / biosynthesis
  • Riboflavin / metabolism*
  • Riboflavin Synthase / chemistry*
  • Riboflavin Synthase / metabolism*
  • Sequence Alignment


  • Ligands
  • Protein Subunits
  • Riboflavin Synthase
  • Riboflavin

Associated data

  • PDB/1HZE
  • PDB/1I18