Streptococcus pneumonia YlxR at 1.35 angstrom shows a putative new fold

The structure of the YlxR protein of unknown function from Streptococcus pn eumonia was determined to 1.35 Angstrom. YlxR is expressed from the nusA/in fB operon in bacteria and belongs to a small protein family (COG2740) that shares a conserved sequence motif GRGA(Y/W). The family shows no significan t amino-acid sequence similarity with other proteins. Three-wavelength diff raction MAD data were collected to 1.7 Angstrom from orthorhombic crystals using synchrotron radiation and the structure was determined using a semiau tomated approach. The YlxR structure resembles a two-layer alpha/beta sandw ich with the overall shape of a cylinder and shows no structural homology t o proteins of known structure. Structural analysis revealed that the YlxR s tructure represents a new protein fold that belongs to the alpha-beta plait superfamily. The distribution of the electrostatic surface potential shows a large positively charged patch on one side of the protein, a feature oft en found in nucleic acid-binding proteins. Three sulfate ions bind to this positively charged surface. Analysis of potential binding sites uncovered s everal substantial clefts, with the largest spanning 3/4 of the protein. A similar distribution of binding sites and a large sharply bent cleft are ob served in RNA-binding proteins that are unrelated in sequence and structure . It is proposed that YlxR is an RNA-binding protein.