Fig. 1. Ribbon representation of Hsp15 colored by conservation. (A) Forty-three eubacterial members of the Hsp15 family were identified by a BLAST search of the non-redundant database and the unfinished microbial databases in July, 1999 (Altschul et al., 1997). Green residues are identical or contain conservative substitutions in at least 50% of the sequences. Residues 4–110 are shown. The portion of the αL loop is labeled with an L. (B) As (A), but oriented with the proposed RNA-binding αL motif in front. This is the orientation of Hsp15 used in all subsequent figures.

Fig. 2. Ribbon diagram of non-crystallographic symmetry mates. Residues 9–57 are colored yellow and represent the proposed αL RNA-binding motif, the remaining residues are in blue. The secondary structure was identified and the drawing rendered using RIBBONS (Carson, 1997).

Fig. 3. Structure-based sequence alignment of the proposed αL RNA-binding motif in heat shock protein 15 kDa (Hsp15), ribosomal protein S4 (S4) and threonyl-tRNA synthetase (Thr-RS). Only the portion of each protein sequence that is structurally similar is shown. The secondary structures as identified by RIBBONS (Carson, 1997) are shown above the sequence alignments. Residues that are >50% conserved or identical within each family are shown in bold upper case letters. Residues in bold green upper case letters are both conserved in at least 50% of the members of each family, and are solvent accessible as determined by XPLOR (Brünger, 1997). Residues that are similar between at least two of the three structures are shaded gray.

Fig. 4. Conservation of surface-exposed residues in the αL motif. (A) Surface electrostatic potential of Hsp15 orientated to show the proposed RNA-binding αL motif facing outwards. This is the orientation identical to that in Figure 1B. The extreme ranges of red (negative) and blue (positive) represent electrostatic potentials of less than –9 to greater than +9 k_bT, where k_b is the Boltzmann constant and T is the temperature. The figure was calculated with GRASP (Nicholls et al., 1991) showing the accessible surface. (B) Surface-exposed residues of Hsp15 that are conserved within the Hsp15 family are shown in green. (C) Surface-exposed residues of ribosomal protein S4 that are conserved within the S4 family are shown in green. Inset is a diagram of the complete S4 protein with the domain homologous to Hsp15 highlighted in red. (D) Surface-exposed residues of threonyl-tRNA synthetase that are conserved within the threonyl-tRNA synthetase family are shown in green. Inset is a diagram of the complete threonyl-tRNA synthetase protein with the domain homologous to Hsp15 highlighted in red.

Fig. 5. The αL motif in three different protein structures. The peptide backbones of three structures, ribosomal protein S4, Hsp15 and threonyl–tRNA, are compared. The region highlighted in color is the αL motif that is shared by all three proteins. (A) Hsp15 with its αL motif highlighted in yellow. (B) Ribosomal protein S4 with its αL motif highlighted in blue. (C) Threonyl-tRNA synthetase with its αL motif highlighted in red. (D) Overlay of residues 9–57 of Hsp15 (yellow), 92–141 of ribosomal protein S4 (blue) and 18–59 of threonyl-tRNA synthetase (red).