title: Flavogenomics--a genomic and structural view of flavin-dependent proteins.
abstract: Riboflavin (vitamin B(2)) serves as the precursor for FMN and FAD in almost all organisms that utilize the redox-active isoalloxazine ring system as a coenzyme in enzymatic reactions. The role of flavin, however, is not limited to redox processes, as ∼ 10% of flavin-dependent enzymes catalyze nonredox reactions. Moreover, the flavin cofactor is also widely used as a signaling and sensing molecule in biological processes such as phototropism and nitrogen fixation. Here, we present a study of 374 flavin-dependent proteins analyzed with regard to their function, structure and distribution among 22 archaeal, eubacterial, protozoan and eukaryotic genomes. More than 90% of flavin-dependent enzymes are oxidoreductases, and the remaining enzymes are classified as transferases (4.3%), lyases (2.9%), isomerases (1.4%) and ligases (0.4%). The majority of enzymes utilize FAD (75%) rather than FMN (25%), and bind the cofactor noncovalently (90%). High-resolution structures are available for about half of the flavoproteins. FAD-containing proteins predominantly bind the cofactor in a Rossmann fold (∼ 50%), whereas FMN-containing proteins preferably adopt a (βα)(8)-(TIM)-barrel-like or flavodoxin-like fold. The number of genes encoding flavin-dependent proteins varies greatly in the genomes analyzed, and covers a range from ∼ 0.1% to 3.5% of the predicted genes. It appears that some species depend heavily on flavin-dependent oxidoreductases for degradation or biosynthesis, whereas others have minimized their flavoprotein arsenal. An understanding of 'flavin-intensive' lifestyles, such as in the human pathogen Mycobacterium tuberculosis, may result in valuable new intervention strategies that target either riboflavin biosynthesis or uptake.
authors.affiliation: Institute of Biochemistry, Graz University of Technology, Graz, Austria. peter.macheroux@tugraz.at
authors.forename: Peter
authors.initials: P
authors.lastname: Macheroux
authors.forename: Barbara
authors.initials: B
authors.lastname: Kappes
authors.forename: Steven E
authors.initials: SE
authors.lastname: Ealick
mesh_terms: D056890:Eukaryota / Q000378:metabolism; D005486:Flavin Mononucleotide / Q000737:chemistry; D005182:Flavin-Adenine Dinucleotide / Q000737:chemistry; D005415:Flavins / Q000378:metabolism; D005420:Flavoproteins / Q000737:chemistry / Q000378:metabolism; D023281:Genomics; D011387:Prokaryotic Cells / Q000378:metabolism; D012256:Riboflavin / Q000737:chemistry
chemical_list: D005415:Flavins; D005420:Flavoproteins; D005182:Flavin-Adenine Dinucleotide; D005486:Flavin Mononucleotide; D012256:Riboflavin