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.