title: Identification of six new photoactive yellow proteins--diversity and structure-function relationships in a bacterial blue light photoreceptor.
abstract: Photoactive yellow proteins (PYP) are bacterial photoreceptors with a Per-Arnt-Sim (PAS) domain fold. We report the identification of six new PYPs, thus nearly doubling the size of this protein family. This extends the taxonomic diversity of PYP-containing bacteria from photosynthetic to nonphotosynthetic bacteria, from aquatic to soil-dwelling organisms, and from Proteobacteria to Salinibacter ruber from the phylum Bacteriodetes. The new PYPs greatly increase the sequence diversity of the PYP family, reducing the most prevalent pair-wise identity from 45% to 25%. Sequence alignments and analysis indicate that all 14 PYPs share a common structure with 13 highly conserved residues that form the chromophore binding pocket. Nevertheless, the functional properties of the PYPs vary greatly--the absorbance maximum extends from 432 to 465 nm, the pK(a) of the chromophore varies from pH 2.8 to 10.2, and the lifetime of the presumed PYP signaling state ranges from 1 ms to 1 h. Thus, the PYP family offers an excellent opportunity to investigate how functional properties are tuned over a wide range, while maintaining the same overall protein structural fold. We discuss the implications of these results for structure-function relationships in the PYP family.
authors.affiliation: Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
authors.forename: Masato
authors.initials: M
authors.lastname: Kumauchi
authors.forename: Miwa T
authors.initials: MT
authors.lastname: Hara
authors.forename: Page
authors.initials: P
authors.lastname: Stalcup
authors.forename: Aihua
authors.initials: A
authors.lastname: Xie
authors.forename: Wouter D
authors.initials: WD
authors.lastname: Hoff
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D014644:Genetic Variation; D006217:Halobacterium / Q000737:chemistry / Q000145:classification; D008027:Light; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020283:Photoreceptors, Microbial / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D011487:Protein Conformation; D016992:Rhodobacter / Q000145:classification
chemical_list: D001426:Bacterial Proteins; D020283:Photoreceptors, Microbial; C050162:photoactive yellow protein, Bacteria