Psuedouridines of S. cervisiae 25S rRNA and equivalent nucleotides in Haloarcula marismortui and E. coli. The snoRNA responsible for guiding a particular 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

snR80

Ψ776

775

-1 to G738 (~A737)

-d

snR8

Ψ960

959

G921

U828

snR43

Ψ966

965

U927

G834

snR8

Ψ986

985

U945

C851

snR49

Ψ990

989

U949

G855

snR5

Ψ1004

1003

C963

U868

snR33

Ψ1042

1041

U1001e

A905

snR81

Ψ1052

1051

C1011

C915

snR44

Ψ1056

1055

C1015

U919

snR82

Ψ1110

1109

G1038

G939

snR5

Ψ1124

1123

G1052

G953

snR3

Ψ2129

2128

G1827

C1771

snR3

Ψ2133

2132

U1831

U1775

snR32

Ψ2191

2190

C1888

C1832

snR191

Ψ2258

2257

Ψ1956*

m3Ψ1915

snR191

Ψ2260

2259

Ψ1958*

Ψ1917

snR3

Ψ2264

2263

C1962*

G1921

snR84

Ψ2266

2265

U1964

U1923

snR86

Ψ2314

2313

U2012

U1971

snR9

Ψ2340

2339

A2038

C1997

snR82

Ψ2349

2348

C2047

C2006

snR82

Ψ2351

2350

C2049

C2008

snR11

Ψ2416

2415

U2115

U2074

snR189

Ψ2735

2730

A2402

G2365

snR34

Ψ2826

2822

U2492

Ψ2457

snR46

Ψ2865

2861

U2531

C2496

snR34

Ψ2880

2876

U2546

U2511

snR10

Ψ2923

2919

U2589

U2554

snR37

Ψ2944

2940

U2610

C2575

snR42

Ψ2975

2971

C2641

C2606

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 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.

dAn equivalent nucleotide is not present in 25 S rRNA; it is in expansion segment #9 (ES9), see Gerbi, S.A. 1996. Expansion segments: Regions of variable size that interrupt the universal core secondary structure of ribosomal RNA. In Ribosomal RNA—Structure, evolution, processing, and function in protein synthesis (eds. R.A. Zimmermann and A.E. Dahlberg), pp.71-87. CRC Press, Boca Raton, FL; Clark, C. G., B. W. Tague, V. C. Ware, and S. A. Gerbi, 1984.

eAccording to Ofengand, 2002 these are equivalent; however, he incorrectly reports as a pseudouridine in H. marismortui there and retracts in Del Campo et al., 2005.

Last update: December 30, 2008 6:55 PM.
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