Streptococcus pneumonia YlxR at 1.35 A shows a putative new fold

Abstract

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.

Figure 1

Sequence alignment of YlxR proteins. Completely conserved residues are marked with an asterix and the GRGA(Y/W) motif is underlined.

Figure 2

Structure of the YlxR protein. The ribbon diagrams of the C^α backbone were prepared with the Molscript (Kraulis, 1991) and Adobe Photoshop programs. The view in (b) was obtained by a 90° rotation of the view in (a) around the x axis. Numbers indicate amino-acid residues.

Figure 3

Electrostatic surface potential of the YlxR protein calculated with the GRASP program (Nicholls et al., 1993). Both positive (a) and negative (b) sides of the protein are shown. Sulfate ions are shown in green. Numbers indicate amino-acid residues.

Figure 4

Clefts and cavities in the structure of YlxR protein were calculated using the program SURFNET (Laskowski, 1995) and displayed with RasMol (Sayle & Milner-White, 1995). Only the four largest cavities are shown (red, 2885 ų; magenta, 497 ų; yellow, 455 ų; blue, 348 ų). The major cavity (red) includes two sulfate ions (sul1 and sul2).