Mapped base methylated nucleotides of S. cervisiae 25S rRNA and equivalent nucleotides in Haloarcula marismortui and E. coli.

S. cerevisiaea

H. marismortuib

E. colic

Modified position in 25S [U53879] d

The modified position reported in several older publications e

 

 

m1A645

m1A644

A628

U571

m5U 956f

m5U 955f

U917

U824

m1A2142

m1A2141

C1840

A1784

m5C2278

m5C2277

G1976

A1936

m3U2634

m3U2633

G2299

U2265

m3U2843

m3U2839

A2509

U2474

m5U2924 g

m5U2920 g

U2590

U2555

a sites from Maden, 1990 and Bakin, Lane, and Ofengand, 1994.

b numbering in PDB entry 1JJ2. Asterisks indicate the corresponding nucleotides not visible in the crystal structure of the large subunit H. marismortui at 2.4 angstroms (Klein, et al., 2001; Ban, et al., 2000).

c numbering and modified nucleotides according to Genbank entry J01695, annotated at the Gutell lab Comparative RNA website (www.rna.icmb.utexas.edu) (Cannone, et al., 2002).

d Cannone, J. J., S. Subramanian, M. N. Schnare, J. R. Collett, L. M. D'Souza, Y. Du, B. Feng, N. Lin, L. V. Madabusi, K. M. Muller, N. Pande, Z. Shang, N. Yu, and R. R. Gutell et al., 2002.

e Numbering according to Ofengand and Bakin, 1997 J. Mol. Biol. 266:246-268 ; Gutell et al., 1993 NAR 21:3055-3074.

f Noted as preliminary in Bakin, Lane, and Ofengand, 1994.

g Noted as preliminary in Bakin, Lane, and Ofengand, 1994. Lapeyre and Purushothoman, 2004 presents data that supports the presence of this modification although in earlier drafts they noted "this modified nucleotide is not present in stoichiometric amount when compared to other modified nucleotides of the A-loop."

 

Mapped base methylated nucleotides of S. cervisiae 18S rRNA and equivalent nucleotides in Haloarcula marismortui and E. coli.

S. cerevisiaea

E. colib

Modified position in 18S [U53879]c

The modified position reported in several older publications d

 

m7G1575

m7G1574

G1338

m26A1781

m26A1780

m26A1518

m26A1782

m26A1781

m26A1519

aSites according to Maden, 1990; Bakin and Ofengand, 1995; Ofengand, J., and M. J. Fournier. 1998. The pseudouridine residues of ribosomal RNA: number, location, biosynthesis, and function. In H. Grosjean and R. Benne (ed.), Modification and Editing of RNA: the Alteration of RNA Structure and Function. ASM Press.

bE. coli numbering according to Genbank entry J01695, annotated at the Gutell lab Comparative RNA website. (Cannone, et al., 2002).

cSequence from Johnston, M., L. Hillier, L. Riles, K. Albermann, B. Andre, W. Ansorge, V. Benes, M. Bruckner, H. Delius, E. Dubois, A. Dusterhoft, K. D. Entian, M. Floeth, A. Goffeau, U. Hebling, K. Heumann, D. Heuss-Neitzel, H. Hilbert, F. Hilger, K. Kleine, P. Kotter, E. J. Louis, F. Messenguy, H. W. Mewes, J. D. Hoheisel, and et al. 1997. accessible at the Saccharomyces Genome Database (Issel-Tarver, L., K. R. Christie, K. Dolinski, R. Andrada, R. Balakrishnan, C. A. Ball, G. Binkley, S. Dong, S. S. Dwight, D. G. Fisk, M. Harris, M. Schroeder, A. Sethuraman, K. Tse, S. Weng, D. Botstein, and J. M. Cherry. 2002.), secondary structure annotated at the Gutell lab Comparative RNA website (Cannone, J. J., S. Subramanian, M. N. Schnare, J. R. Collett, L. M. D'Souza, Y. Du, B. Feng, N. Lin, L. V. Madabusi, K. M. Muller, N. Pande, Z. Shang, N. Yu, and R. R. Gutell et al., 2002.)

dnumbering according to Bakin and Ofengand, 1995 NAR 23:3290-3294.

Last update: October 16, 2006 3:37 PM.