Nucleic acid recognition by OB-fold proteins

Abstract

The OB-fold domain is a compact structural motif frequently used for nucleic acid recognition. Structural comparison of all OB-fold/nucleic acid complexes solved to date confirms the low degree of sequence similarity among members of this family while highlighting several structural sequence determinants common to most of these OB-folds. Loops connecting the secondary structural elements in the OB-fold core are extremely variable in length and in functional detail. However, certain features of ligand binding are conserved among OB-fold complexes, including the location of the binding surface, the polarity of the nucleic acid with respect to the OB-fold, and particular nucleic acid-protein interactions commonly used for recognition of single-stranded and unusually structured nucleic acids. Intriguingly, the observation of shared nucleic acid polarity may shed light on the longstanding question concerning OB-fold origins, indicating that it is unlikely that members of this family arose via convergent evolution.

Figure 1

The canonical OB-fold domain. The OB-fold from AspRS is shown in stereo as representative of the ideal OB-fold domain. From the N terminus to the C terminus, strand β1 is shown in red, β2 in orange, β3 in yellow, the helix between β3 and β4 in green, β4 in blue, and β5 in violet. An α-helix, which is found in half of the OB-folds in these complexes, is shown in white at the top of the figure, just N-terminal to strand β1. Variable loops between strands are indicated in black text.

Figure 2

(Continued) Structures of OB-fold/nucleic acid complexes. The high-resolution structures of several OB-fold proteins bound to nucleic acids. The individual OB-fold domains are highlighted in rainbow colors to illustrate the modularity of the domain. (a) OnTEBP ternary complex, (b) EcRho, (c) human RPA, (d) RecG, (e) EcAspRS, (f) Cdc13, (g) EcSSB, (h) L2 in the large subunit of the ribosome, (i) S12 (green), S17 (blue), and IF1 (magenta) in the ribosomal small subunit.

Figure 2(continued)

Figure 3

Figure 3(opposite, above)

Comparison of ligand binding in the OB-fold domains. The 14 independent OB-fold domains are depicted in a common orientation based on superimposition with the N-terminal OB-fold of RPA. Secondary structure is rainbow colored beginning with violet at the N terminus and ending with red at the C terminus. Nucleic acids that are within 3.5 Å of the relevant fold are rendered as ball-and-stick figures. OB-folds were aligned with LSQMAN. (a) OnTEBP α1, (b) Cdc13, (c) OnTEBP α2, (d) OnTEBP β, (e) RPA-A, (f) RPA-B, (g) EcSSB, (h) RecG, (i) EcAspRS, (j) EcRho, (k) IF1, (l) L2, (m) S12, (n) S17.

Figure 4

Conformational change upon ligand binding. The bound OB-fold complex is shown in slate blue, while the unbound protein is shown in green. (a) The N-terminal OB-fold of human RPA. (b) The OB-fold from EcRho transcriptional terminator.

Figure 5

Structure-based sequence alignment of OB-fold domains. (a) The AspRS OB-fold is depicted with key residues highlighted in color. Hydrophobic residues that pack in the top layer of the barrel’s interior are shown in orange, the middle layer in violet, the bottom layer in dark blue, and the "extra-bottom" layer in light blue. Two glycines are shown in green, while the conspicuous solvent-exposed hydrophobic side chain in strand β3 is shown in dark gray and rendered as a ball-and-stick figure. The DNA that interacts with this residue is rendered as ball-and-stick in CPK colors. A conserved polar residue found after strand β3 is highlighted in magenta.(b) In color, a structure-based sequence alignment of the OB-folds is augmented below with the corresponding secondary structures in black and white. Variable loop regions have, for the most part, been omitted and their length is indicated by number of amino acids in parentheses. Helices are shown as black cylinders, β-strands are shown as bars with arrows, and turns are shown as blue wedges. Regions of secondary structure significantly conserved among the OB-folds are boxed in thick black lines. Completely conserved hydrophobic residues are highlighted with gray columns, while positions with 75% conserved hydrophobicity are highlighted with yellow columns. A conserved polar position after strand β3 is highlighted with a magenta column. Strands are indicated above and below the alignment in blue. An orange T, a violet M, and a dark blue B indicate the top, middle, and bottom interior residues, respectively. The additional bottom residues are indicated by light blue xB text. Proline residues are colored green, acidic residues (aspartate and glutamate) are colored red, and basic residues (lysine and arginine) are colored blue. Asterisks (^*) indicate two well-conserved glycines, and an ampersand (&) indicates a conspicuous solvent-exposed hydrophobic residue. [1] gp32, [2] OnTEBP β, [3] Cdc13, [4] L2, [5] Rho, [6] EcSSB, [7] EcAspRS, [8] OnTEBP α1, [9] RPA-A, [10] RecG, [11] OnTEBP α2, [12] RPA-B, [13] S12, [14] S17, [15] IF1.

Figure 5(Continued)