Modomics - A Database of RNA Modifications

Full name:	Ribosomal RNA large subunit methyltransferase D
Synonym:	RumA, YgcA
GI:	388478792
Orf:	ygcA, b2776
COG:	COG2265
UniProt:	P55138
Structures:	\| 2BH2 \| 1UWV \|
Complex:
Enzyme type:	methyltransferase
Position of modification - modification:	l:1939(1939) - m5U

Comments:

RlmD (formerly RumA) methylates the conserved U1939 in a loose hairpin ‘70’ located between conserved hairpins 69 and 71 in domain IV the large subunit rRNA. Recombinant E.coli RlmD was shown to be active in vitro on a small 40 nucleotides long fragment of 23S rRNA encompassing U1939. It displays a N-terminal TRAM domain, a five-stranded beta barrel architecture characteristic of an oligosaccharide/ oligonucleotide binding fold and a central domain contains a [Fe(4)S(4)] cluster coordinated by four conserved cysteine residues. The C-terminal domain displays the typical SAM-dependent methyltransferase fold. AdoMet is the methyl group donor. The paralog enzyme in B. subtilis (RlmCD) is multisite specific, while in Archaea, no RlmD paralog has been identified. The presence of m5U1939 methylation in 23S rRNA is not essential but helps to improve ribosome performance.

Protein sequence:

MAQFYSAKRRTTTRQIITVSVNDLDSFGQGVARHNGKTLFIPGLLPQENAEVTVTEDKKQYARAKVVRRLSDSPERETPRCPHFGVCGGCQQQHASVDLQ
QRSKSAALARLMKHDVSEVIADVPWGYRRRARLSLNYLPKTQQLQMGFRKAGSSDIVDVKQCPILAPQLEALLPKVRACLGSLQAMRHLGHVELVQATSG
TLMILRHTAPLSSADREKLERFSHSEGLDLYLAPDSEILETVSGEMPWYDSNGLRLTFSPRDFIQVNAGVNQKMVARALEWLDVQPEDRVLDLFCGMGNF
TLPLATQAASVVGVEGVPALVEKGQQNARLNGLQNVTFYHENLEEDVTKQPWAKNGFDKVLLDPARAGAAGVMQQIIKLEPIRIVYVSCNPATLARDSEA
LLKAGYTIARLAMLDMFPHTGHLESMVLFSRVK

Enzymatic activities:

Reaction	Substrate	Type	Position
U:m5U	rRNA (r)	LSU/23S/prokaryotic cytosol	1939

Publications:

Title	Authors	Journal	Details	PubMed Id	DOI
Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coli.	Agarwalla S, Kealey JT, Santi DV, Stroud RM	J Biol Chem	[details]	11779873	-
A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.	Lee TT, Agarwalla S, Stroud RM	Cell	[details]	15766524	-
Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase.	Lee TT, Agarwalla S, Stroud RM	Structure	[details]	15016356	-
Mutagenesis of the modified bases, m(5)U1939 and psi2504, in Escherichia coli 23S rRNA.	Persaud C, Lu Y, Vila-Sanjurjo A, Campbell JL, Finley J, O'Connor M	Biochem Biophys Res Commun	[details]	20067766	-