title: Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins.
abstract: E. coli YhbY belongs to a conserved family of hypothetical proteins represented in eubacteria, archaea, and plants (Pfam code UPF0044). Three maize proteins harboring UPF0044-like domains are required for chloroplast group II intron splicing, and bioinformatic data suggest a role for prokaryotic UPF0044 members in translation. The crystal structure of YhbY has been determined. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Modeling studies indicate that the same surface is highly basic in all members of UPF0044, suggesting a conserved RNA binding surface. Taken together, the evidence suggests that members of UPF0044 constitute a previously unrecognized class of RNA binding domain.
authors.affiliation: Institute of Molecular Biology, 1229 University of Oregon, Eugene, OR 97403, USA.
authors.forename: Gerard J
authors.initials: GJ
authors.lastname: Ostheimer
authors.forename: Alice
authors.initials: A
authors.lastname: Barkan
authors.forename: Brian W
authors.initials: BW
authors.lastname: Matthews
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics; D007438:Introns; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012313:RNA / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism; D017386:Sequence Homology, Amino Acid
chemical_list: D029968:Escherichia coli Proteins; D012336:RNA, Ribosomal, 16S; D016601:RNA-Binding Proteins; C474287:YhbY protein, E coli; D012313:RNA