title: A structural code for discriminating between transcription signals revealed by the feast/famine regulatory protein DM1 in complex with ligands.
abstract: Feast/famine regulatory proteins (FFRPs) comprise the largest group of archaeal transcription factors. Crystal structures of an FFRP, DM1 from Pyrococcus, were determined in complex with isoleucine, which increases the association state of DM1 to form octamers, and with selenomethionine, which decreases it to maintain dimers under some conditions. Asp39 and Thr/Ser at 69-71 were identified as being important for interaction with the ligand main chain. By analyzing residues surrounding the ligand side chain, partner ligands were identified for various FFRPs from Pyrococcus, e.g., lysine facilitates homo-octamerization of FL11, and arginine facilitates hetero-octamerization of FL11 and DM1. Transcription of the fl11 gene and lysine synthesis are regulated by shifting the equilibrium between association states of FL11 and by shifting the equilibrium toward association with DM1, in response to amino acid availability. With FFRPs also appearing in eubacteria, the origin of such regulation can be traced back to the common ancestor of all extant organisms, serving as a prototype of transcription regulations, now highly diverged.
authors.affiliation: National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Center 6-10, Higashi 1-1-1, Tsukuba 305-8566, Japan.
authors.forename: Hideyasu
authors.initials: H
authors.lastname: Okamura
authors.forename: Katsushi
authors.initials: K
authors.lastname: Yokoyama
authors.forename: Hideaki
authors.initials: H
authors.lastname: Koike
authors.forename: Mitsugu
authors.initials: M
authors.lastname: Yamada
authors.forename: Ai
authors.initials: A
authors.lastname: Shimowasa
authors.forename: Mamiko
authors.initials: M
authors.lastname: Kabasawa
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Kawashima
authors.forename: Masashi
authors.initials: M
authors.lastname: Suzuki
mesh_terms: D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001120:Arginine / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D019281:Dimerization; D007532:Isoleucine / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019711:Pyrococcus / Q000378:metabolism; D012645:Selenomethionine / Q000737:chemistry / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D019843:Archaeal Proteins; D008024:Ligands; D014157:Transcription Factors; D007532:Isoleucine; D001120:Arginine; D012645:Selenomethionine