Modomics - A Database of RNA Modifications

ID Card:

Full name:	Ribosomal RNA Cytosine Methyltransferase 1
Synonym:	Ynl022c
GI:	398365407
Orf:	N2815
COG:	COG0144
UniProt:	P53972
Alpha Fold Predicted Structure:	AF-P53972-F1
Enzyme type:	methyltransferase
Position of modification - modification:	l:2278(1935) - m5C

Protein sequence:

MNFYRDATWVLEDIEKEAAKERISGSMQTLVLKSCKRYKLKSNPKHIYAVLDSCWKYKPYLEKVMKKAHILEDIPKKKGKPLFSRLTLLLLCHDLLLSKQKRIQMGKHPIKDYVLKFKSPLHSEMVKLKLKLKVRELSELVLSEDISNDLPPVRWIRINPLKCHPNGETEPVLAELRKKFTLKVDKWSELVPGSIYYDEFIPNLFGIHPSDKITAHELYKHGKIIIQDRASCFPAHILNPGPSDIVIDSCSAPGNKTTHTASYIYPEPPKDNNTRIYAFEKDPERAKVLQKMIKIAGCSPNISVNVGDFTKLATPEKYKDVTCFIVDPSCSGSGIFGRKFFDSFNRRKIDDKDDDGGIVPDEQEEFIAKEELQTRLAKLSSFQFQMVKHAMSFPAAKKIVYSTCSIHAEENERVVIDLLLDKSVREWGWKVAPKREVIPSWPRRGKVEEFEEVFRDGVTYDPQQLAEGCIRALPKSDGGIGFFAVCFERD

Comments:

The loss of m5C2278 results in anisomycin hypersensitivity. A combined loss of m5C2278 and Gm2288 cause dramatic ribosome instability, resulting in loss of 60S ribosomal subunits. Rcm1 interacts with Trm112 but deletion of Trm112 has no significant effect on the modification state of cytosine 2278.

Reaction	Substrate	SubstrateType	Position	(Anti)Codon	Modified (Anti)Codon	Amino Acid Change	Transcript Name	Transcript Region	Cellular Localization	References
C:m5C	rRNA (r)	LSU-L/25S/eukaryotic cytosol	2278							23913415

Alpha Fold Predicted Structure:

Clear Selection and Reset Camera

Protein sequence:

M N F Y R D A T W V L E D I E K E A A K E R I S G S M Q T L V L K S C K R Y K L K S N P K H I Y A V L D S C W K Y K P Y L E K V M K K A H I L E D I P K K K G K P L F S R L T L L L L C H D L L L S K Q K R I Q M G K H P I K D Y V L K F K S P L H S E M V K L K L K L K V R E L S E L V L S E D I S N D L P P V R W I R I N P L K C H P N G E T E P V L A E L R K K F T L K V D K W S E L V P G S I Y Y D E F I P N L F G I H P S D K I T A H E L Y K H G K I I I Q D R A S C F P A H I L N P G P S D I V I D S C S A P G N K T T H T A S Y I Y P E P P K D N N T R I Y A F E K D P E R A K V L Q K M I K I A G C S P N I S V N V G D F T K L A T P E K Y K D V T C F I V D P S C S G S G I F G R K F F D S F N R R K I D D K D D D G G I V P D E Q E E F I A K E E L Q T R L A K L S S F Q F Q M V K H A M S F P A A K K I V Y S T C S I H A E E N E R V V I D L L L D K S V R E W G W K V A P K R E V I P S W P R R G K V E E F E E V F R D G V T Y D P Q Q L A E G C I R A L P K S D G G I G F F A V C F E R D

Secondary Structure Alphabet

G: 3-turn helix (3₁₀helix)
H: α-helix
I: 𝝅-helix (5 - turn helix)
T: Hydrogen Bonded Turn
B: β-sheet
S: Bend
C: Coil (residues not present in any of the above conformations)
N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files	AF-P53972-F1.pdb
Alpha Fold Pdbx/mmCIF Files	AF-P53972-F1.cif
DSSP Secondary Structures	P53972.dssp

Publications:

Title	Authors	Journal	Details	PubMed Id	DOI
Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively.	Sharma S, Yang J, Watzinger P, Kotter P, Entian KD...	Nucleic Acids Res	[details]	23913415	-
Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan.	Schosserer M, Minois N, Angerer TB, Amring M, Dellago H, Harreither E, Calle-Perez A, Pircher A, Gerstl MP, Pfeifenberger S, Brandl C, Sonntagbauer M, Kriegner A, Linder A, Weinhausel A, Mohr T, Steiger M, Mattanovich D, Rinnerthaler M, Karl T, Sharma S, Entian KD, Kos M, Breitenbach M, Wilson IB, Polacek N, Grillari-Voglauer R, Breitenbach-Koller L, Grillari J...	Nat Commun	[details]	25635753	-

Links:

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