Summary: RNA 2'-O ribose methyltransferase substrate binding
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RNA 2'-O ribose methyltransferase substrate binding Provide feedback
This domain is a RNA 2'-O ribose methyltransferase substrate binding domain.
Internal database links
|Similarity to PfamA using HHSearch:||TSNR_N|
This tab holds annotation information from the InterPro database.
InterPro entry IPR013123
Most cellular RNAs undergo a number of post-transcriptional nucleoside modifications. While the biological role of many of these modifications is unknown, some have been shown to be necessary for cell growth or for resistance to antibiotics [PUBMED:8266080, PUBMED:9187657]. One of the most common modifications is 2'O-ribose methylation catalysed by the RNA 2'O-ribose methyltransferases, a large enzyme family that transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose [PUBMED:9917067].
This entry represents a substrate-binding domain found in a variety of bacterial and mitochondrial RNA 2'-O ribose methyltransferases. These include the bacterial enzyme RlmB, which specifically methylates the conserved nucleotide guanosine 2251 in 23S RNA, and PET56, which specifically methylates the equivalent guanosine in mitochondrial 21S RNA [PUBMED:11698387, PUBMED:8266080]. This domain forms a four-stranded mixed beta sheet similar to that found in other RNA binding enzymes [PUBMED:12377117]. It shows considerable conformational flexibility which is thought to be important for its ability to bind RNA.
|Molecular function||methyltransferase activity (GO:0008168)|
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The members of this clan are all involved in binding to ribose sugar of RNA. Indeed, the key RNA binding residues are conserved across the different families . Members of this clan form mixed alpha-helical and beta-sheet structures .
The clan contains the following 5 members:eRF1_3 PELOTA_1 Ribosomal_L7Ae RNase_P_pop3 SpoU_sub_bind
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Pfam-B_742 (release 16.0)|
|Number in seed:||97|
|Number in full:||3670|
|Average length of the domain:||75.50 aa|
|Average identity of full alignment:||21 %|
|Average coverage of the sequence by the domain:||26.01 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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_sub_bind domain has been found. There are 9 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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