Modified Nucleosides of Escherichia coli Ribosomal RNA

Figure 1

The modified nucleosides found in E. coli rRNA. Ψ, 5−ribosyluracil (pseudouridine); m3Ψ, 3-methylpseudouridine; m3U, 3-methyluridine; m5U, 5-methyluridine; hU, 5,6-dihydrouridine; m4C, N4-methylcytidine; m5C, 5-methylcytidine; Nm, 2′-OCH3-N (N = A, G, U, or C); m2A, 2-methyladenosine; m6A, N6-methyladenosine; m6 2A, N6-dimethyladenosine; m1G, 1-methylguanosine; m2G, N2-methylguanosine; m7G, 7-methylguanosine.

Figure 2

Location of the modified nucleosides of 16S rRNA. The secondary structure is modified from the Comparative RNA Web Site (http://www.rna.icmb.utexas.edu/). Modified nucleoside positions are as indicated.

Figure 3

Location of the modified nucleosides of 23S rRNA. The secondary structure was obtained as in Fig. 2 and is shown with the modified nucleosides as indicated.

Figure 4

Location of modified nucleosides on the 30S ribosome. (A) View from the interface side of the ribosomal subunit. (B) View in A rotated by 90°. The three-dimensional structure of the 16S RNA of the 30S ribosome of T. thermophilus ( 54 ; Protein Data Bank [PDB] entry 1J5E) is shown with all proteins removed and the phosphodiester backbone represented by a continuous line. Ψ residues are shown as 6-Å-diameter red spheres. Methylated nucleosides are shown as 6-Å-diameter green spheres irrespective of whether they are purine or pyrimidine derived or base methylated versus ribose methylated. All spheres are centered on the glycosyl N of the base. The identifying numbers are listed in Table 1 and 2 .

Figure 5

Location of modified nucleosides on the 50S ribosome. (A) View from the interface side of the ribosomal subunit. (B) View in panel A rotated by 90°. The three-dimensional structure of the 23S RNA of the 50S ribosome of Deinococcus radiodurans ( 55 ; PDB entry 1NKW) is shown the same way as in Fig. 4 . Ψ and methylated nucleosides are denoted as in Fig. 4 . Dihydrouridine and the unidentified modified C2501 are shown as a light blue and yellow 6-Å sphere, respectively. All spheres are centered on the glycosyl N of the base. Residue 2057 (cyan sphere marked by black triangle), 2058 and 2059 (cyan spheres), 2062 (orange sphere), 2609 (orange sphere marked by black triangle), and 2611 (black sphere) are all located at the interface entrance to the exit tunnel ( 56 , 57 ). These spheres are 3 Å in diameter to conserve space.

Figure 6

Multiple sequence alignment of E. coli RluA and RsuA family rRNA Ψ synthases. Five of the synthases have an N-terminal domain similar to the RNA-binding domain of ribosomal protein S4 (grey bar). The five motifs described by Del Campo et al. ( 20 ) are indicated with different colored bars matching the colored ribbon segments in Fig. 8 . The S4 domain secondary structure (above) is from the crystal structure of RsuA ( 18 ; PDB entry 1KSK). The Ψ synthase domain secondary structure (above) is from the crystal structures of RsuA and RluD ( 20 ; PDB entry 1QYU) by using those elements consistent with both structures. Conserved residues are shown in bold face with conserved active-site residues highlighted in yellow and other identical residues highlighted in light blue. Numbers to the left of each line denote the sequence position of the first residue shown. Dashes indicate gaps in sequence, and numbers in parentheses indicate the number of residues that are not shown in the alignment.

Figure 7

Comparison of RluD and RsuA crystal structures. (A) Ribbon cartoon of RsuA ( 18 ; PDB entry 1KSK) in blue superposed onto RluD ( 20 ; PDB entry 1QYU) in orange using DALI ( 63 ). Nonoverlapping domains are labeled. (B) Superposed side chains (starting at the C?) from the five conserved active-site residues of RluD and RsuA (highlighted in yellow in Fig. 6 ). The N, C, C?, C?, and O atoms of all five residues from RsuA were superposed onto the equivalent five residues of RluD using LSQMAN ( 64 ). Colors are the same as in panel A. The figure was generated with PyMOL ( 65 ).

Figure 8

Location of the five Ψ synthase motifs on the structure of RluD. Ribbon cartoon of RluD is light gray. Motifs I, II, IIa, III, and IIIa are the same colors as the bars in Fig. 6 . The side chains of the five conserved active-site residues (highlighted yellow in Fig. 6 ) are shown in ball-and-stick representation and are the same color as the motif to which they belong. The figure was generated with PyMOL ( 65 ).

Reprinted with permission from reference 20 .