Ribose methylated nucleotides of S. cervisiae 25S rRNA and equivalent nucleotides in Haloarcula marismortui and E. coli. The snoRNA responsible for guiding a particular modification or protein that catalyzes the modification in yeast is also included.

 

S. cerevisiae

H. marismortuib

E. colic

snoRNA

Modified position in 25S [U53879] a

The modified position reported in several older publications

The modified position is reported with following number in Lowe Database (July 2006 version)

U18

Am649

648

647

A632

A575

U18

Cm650

649

648

C633

U576

snR58

Cm663

662

661

G646

U589

snR39b

Gm805

804

803

G765

G674

snR39 (snR59)

Am807

806

805

A767

A676

snR60

Am817

816

815

U777

U686

snR50

Gm867

866

865

G828

C736

snR72

Am876

875

874

U837

U744

snR40

Um898

897

896

C859

U766

snR60

Gm908

907

906

G869

G776

snR61

Am1133

1132

1131

C1061

U963

U24

Cm1437

1436

1435

C1360

G1256

U24

Am1449

1448

1447

A1372

A1268

U24

Gm1450

1449

1448

G1373

A1269

snR62

Um1888

1886

1886

C1734

C1656

snR76

Cm2197

2196

2195

C1894

C1838

snR47

Am2220

2219

2218

G1917

-1 to G1869 (~C1868)d

snR63

Am2256

2255

2254

A1954*

A1913

snR13

Am2280

2279

2278

A1978

A1937

snR13

Am2281

2280

2279

G1979

A1938

snR75

Gm2288

2287

2286

G1986

G1945

snR64

Cm2337

2336

2335

C2035

C1994

snR65

Um2347

2346

2345

G2045

G2004

snR66

Um2417

2416

2415

U2116

U2075

snR78

Um2421

2420

2419

U2120

U2079

snR67

Gm2619

2618

2616

G2284

Gm2251

snR68

Am2640

2639

2637

A2305

G2271

snR67

Um2724

2720

2721

U2390

U2356

snR51

Um2729

2724

2726

C2396

C2359

snR48

Gm2791

2787

2788

U2457

C2420

snR48

Gm2793

2789

2790

G2459

C2422

snR38

Gm2815

2811

2812

G2481

G2446

snR52

Um2921

2917

2918

Um2587

Um2552

Spb1p

Gm2922

2918

2919e

Gm2588

G2553

snR71

Am2946

2942

2943

A2612

A2577

snR69

Cm2948

2944

2945

C2614

C2579

snR73

Cm2959

2955

2956

C2625

A2590

aSequence 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.)

bNumbering as 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, D. J., T. M. Schmeing, P. B. Moore, and T. A. Steitz., 2001 and Ban, N., P. Nissen, J. Hansen, P. B. Moore, and T. A. Steitz., 2000). Modified nucleotides are indicated according to Kirpekar, et al. 2005.

cNumbering of modified nucleotides according to Genbank entry J01695, annotated at the Gutell lab Comparative RNA website.

a,b,cAligned using data from the rRNA WWW server.

dHowever, because nts 1865-1868 of the large subunit are disordered and not visible in the 5.5 Å T. thermophilus model (PDB code:1GIY) that uses E. coli numbering, nt 1869 is highlighted as an approximation in the 3D map that uses that model. In the 2.8 Å T. thermophilus model (PDB code:1GIY) that uses E. coli numbering the nts 1867 through 1875 of the large subunit are not visible and so no nucleotide is highlighted in the 3D map using that model.

eThis position was assigned to snR52 in Lowe and Eddy, 1999 as it was adjacent a site guided by snR52 and other snoRNAs had been shown to guide adjacent sites as well; however, the complexity in this region made confirmation by experiment difficult. Later assigned to Spb1p in Lapeyre anr Purushothaman, 2004.

Last update: October 25, 2007 5:37 PM.
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