title: Solution structure of HI0257, a bacterial ribosome binding protein.
abstract: A novel bacterial ribosome binding protein, protein Y (also known as YfiA), was recently shown to reside at the 30S/50S subunit interface and to stabilize the ribosomal 70S complex against dissociation at low magnesium ion concentrations. We report here the three-dimensional NMR structure in solution of a homologue from Haemophilus influenzae, HI0257, that has 64% sequence identity to protein Y. The 107 residue protein has a beta-alpha-beta-beta-beta-alpha folding topology with two parallel alpha-helices packed against the same side of a four-stranded beta-sheet. The closest structural relatives are proteins with the double-stranded RNA-binding domain (dsRBD) motif although there is little (<10%) sequence homology. The most immediate differences between the dsRBD and HI0257 structures are that (1) HI0257 has a larger beta-sheet motif with an extra beta-strand at the N-terminus, (2) the helices are parallel in HI0257 but at an angle of about 30 degrees to each other in the dsRBD, and (3) HI0257 lacks the extended loop commonly seen between the first and second beta-strands of the dsRBD. Further, an analysis of the surface electrostatic potential in HI0257 and the dsRBD family reveals significant differences in the location of contiguous positively (and negatively) charged regions. The structural data, in combination with sequence analysis of HI0257 and its homologues, suggest that the most likely mode of RNA recognition for HI0257 may be distinct from that of the dsRBD family of proteins.
authors.affiliation: Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville Maryland 20850, USA.
authors.forename: L
authors.initials: L
authors.lastname: Parsons
authors.forename: E
authors.initials: E
authors.lastname: Eisenstein
authors.forename: J
authors.initials: J
authors.lastname: Orban
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins; D006193:Haemophilus influenzae; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D017434:Protein Structure, Tertiary; D016601:RNA-Binding Proteins / Q000737:chemistry*; D012269:Ribosomal Proteins / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D012996:Solutions
chemical_list: D001426:Bacterial Proteins; C436712:HI0257 protein, Haemophilus influenzae; D016601:RNA-Binding Proteins; D012269:Ribosomal Proteins; D012996:Solutions; C499682:YfiA protein, bacteria