Summary: SpoU rRNA Methylase family
SpoU rRNA Methylase family Provide feedback
This family of proteins probably use S-AdoMet.
Persson BC, Jager G, Gustafsson C; , Nucleic Acids Res 1997;25:4093-4097.: The spoU gene of escherichia coli , the fourth gene of the spoT operon, is essential for tRNA (Gm18) 2 ' - O -methyltransferase activity. PUBMED:9321663 EPMC:9321663
Internal database links
|Similarity to PfamA using HHSearch:||Methyltrn_RNA_4|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001537The spoU gene of Escherichia coli codes for a protein that shows strong similarities to previously characterised 2'-O-methyltransferases [PUBMED:9321663, PUBMED:8265370]. The Pet56 protein of Saccharomyces cerevisiae has been shown to be required for ribose methylation at a universally conserved nucleotide in the peptidyl transferase centre of the mitochondrial large ribosomal RNA (21S rRNA). Cells reduced in this activity were deficient in formation of functional large subunits of the mitochondrial ribosome. The Pet56 protein catalyzes the site-specific formation of 2'-O-methylguanosine on in vitro transcripts of both mitochondrial 21S rRNA and E. coli 23S rRNA providing evidence for an essential modified nucleotide in rRNA [PUBMED:8266080].
|Molecular function||RNA binding (GO:0003723)|
|RNA methyltransferase activity (GO:0008173)|
|Biological process||RNA processing (GO:0006396)|
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A distinct class of methylases that includes the SpoU and TrmD superfamilies and two superfamilies of predicted methylases defined by the YbeA and MJ0421 proteins in bacteria and archaea, respectively  (PFAM:PF00588 PFAM:PF01746). SPOUT is structurally distinct compared to more classical methyltransferases . More specifically, the members of this clan form alpha/beta knots. Knots are extremely rare in protein structures as they pose a folding problem. The mechanism that allow a domain to be folded as a knot are unclear, but are discussed in  and reference therein. All members with known structure form homodimers.
The clan contains the following 11 members:DUF2122 Methyltrans_RNA Methyltrn_RNA_2 Methyltrn_RNA_3 Methyltrn_RNA_4 RNA_Me_trans SpoU_methylase SPOUT_MTase SPOUT_MTase_2 Trm56 tRNA_m1G_MT
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Seed source:||MRC-LMB Genome group|
|Number in seed:||139|
|Number in full:||17854|
|Average length of the domain:||141.80 aa|
|Average identity of full alignment:||26 %|
|Average coverage of the sequence by the domain:||56.74 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SpoU_methylase domain has been found. There are 41 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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