Taxonomic distribution of proteins containing SpoU_sub_bind domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing SpoU_sub_bind domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

The yeast Saccharomyces cerevisiae YDL112w ORF encodes the putative2'-O-ribose methyltransferase catalyzing the formation of Gm18 in tRNAs.

Cavaille J, Chetouani F, Bachellerie JP
RNA. 1999; 5: 66-81

The protein sequences of three known RNA 2'-O-ribose methylases were usedas probes for detecting putative homologs through iterative searches ofgenomic databases. We have identified 45 new positive Open Reading Frames(ORFs), mostly in prokaryotic genomes. Five complete eukaryotic ORFs werealso detected, among which was a single ORF (YDL112w) in the yeastSaccharomyces cerevisiae genome. After genetic depletion of YDL112w, weobserved a specific defect in tRNA ribose methylation, with the completedisappearance of Gm18 in all tRNAs that naturally contain thismodification, whereas other tRNA ribose methylations and the complexpattern of rRNA ribose methylations were not affected. The tRNA G18methylation defect was suppressed by transformation of the disruptedstrain with a plasmid allowing expression of YDL112wp. The formation ofGm18 on an in vitro transcript of a yeast tRNASer naturally containingthis methylation, which was efficiently catalyzed by cell-free extractsfrom the wild-type yeast strain, did not occur with extracts from thedisrupted strain. The protein encoded by the YDL112w ORF, termed Trm3(tRNA methylation), is therefore likely to be the tRNA (Gm18) ribosemethylase. In in vitro assays, its activity is strongly dependent on tRNAarchitecture. Trm3p, the first putative tRNA ribose methylase identifiedin an eukaryotic organism, is considerably larger than its Escherichiacoli functional homolog spoU (1,436 amino acids vs. 229 amino acids), orany known or putative prokaryotic RNA ribose methyltransferase. Homologsfound in human (TRP-185 protein), Caenorhabditis elegans and Arabidopsisthaliana also exhibit a very long N-terminal extension not related to anyprotein sequence in databases.

Solution structure of an rRNA methyltransferase (ErmAM) that confersmacrolide-lincosamide-streptogramin antibiotic resistance.

Yu L, Petros AM, Schnuchel A, Zhong P, Severin JM, Walter K, Holzman TF, Fesik SW
Nat Struct Biol. 1997; 4: 483-9

The Erm family of methyltransferases is responsible for the development ofresistance to the macrolide-lincosamide-streptogramin type B (MLS)antibiotics. These enzymes methylate an adenine of 23S ribosomal RNA thatprevents the MLS antibiotics from binding to the ribosome and exhibitingtheir antibacterial activity. Here we describe the three-dimensionalstructure of an Erm family member, ErmAM, as determined by NMRspectroscopy. The catalytic domain of ErmAM is structurally similar tothat found in other methyltransferases and consists of a seven-strandedbeta-sheet flanked by alpha-helices and a small two-stranded beta-sheet.In contrast to the catalytic domain, the substrate binding domain isdifferent from other methyltransferases and adopts a novel fold thatconsists of four alpha-helices.

Functional requirement of a site-specific ribose methylation in ribosomalRNA.

Sirum-Connolly K, Mason TL
Science. 1993; 262: 1886-9

The product of the PET56 nuclear gene of Saccharomyces cerevisiae wasshown to be required for ribose methylation at a universally conservednucleotide in the peptidyl transferase center of the mitochondrial largeribosomal RNA (21S rRNA). Cells reduced in this activity were deficient information of functional large subunits of the mitochondrial ribosome. Thepurified Pet56 protein catalyzed the site-specific formation of2'-O-methylguanosine on in vitro transcripts of both mitochondrial 21SrRNA and Escherichia coli 23S rRNA. These results provide evidence for anessential modified nucleotide in rRNA.