Streptococcus pneumonia YlxR at 1.35 A shows a putative new fold.
The structure of the YlxR protein of unknown function from Streptococcus pneumonia was determined to 1.35 A. YlxR is expressed from the nusA/infB operon in bacteria and belongs to a small protein family (COG2740) that shares a conserved sequence motif GRGA(Y/W). The family shows no significant amino-acid sequence similarity with other proteins. Three-wavelength diffraction MAD data were collected to 1.7 A from orthorhombic crystals using synchrotron radiation and the structure was determined using a semi-automated approach. The YlxR structure resembles a two-layer alpha/beta sandwich with the overall shape of a cylinder and shows no structural homology to proteins of known structure. Structural analysis revealed that the YlxR structure 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 often found in nucleic acid-binding proteins. Three sulfate ions bind to this positively charged surface. Analysis of potential binding sites uncovered several substantial clefts, with the largest spanning 3/4 of the protein. A similar distribution of binding sites and a large sharply bent cleft are observed in RNA-binding proteins that are unrelated in sequence and structure. It is proposed that YlxR is an RNA-binding protein.
Osipiuk
J
J
Argonne National Laboratory, Structural Biology Center, Biosciences Division, IL 60439, USA.
Górnicki
P
P
Maj
L
L
Dementieva
I
I
Laskowski
R
R
Joachimiak
A
A
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D003460:Crystallization; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D016601:RNA-Binding Proteins; D017386:Sequence Homology, Amino Acid; D013296:Streptococcus pneumoniae / Q000737:chemistry*
D001426:Bacterial Proteins; D016601:RNA-Binding Proteins; C441638:YlxR protein, Streptococcus pneumonia