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13  structures 7768  species 0  interactions 12483  sequences 31  architectures

Family: SpoU_sub_bind (PF08032)

Summary: RNA 2'-O ribose methyltransferase substrate binding

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

RNA 2'-O ribose methyltransferase substrate binding Provide feedback

This domain is a RNA 2'-O ribose methyltransferase substrate binding domain.

Internal database links

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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan PELOTA (CL0101), which has the following description:

The members of this clan are all involved in binding to ribose sugar of RNA[1]. Indeed, the key RNA binding residues are conserved across the different families [1]. Members of this clan form mixed alpha-helical and beta-sheet structures [1][2].

The clan contains the following 7 members:

eRF1_3 PELOTA_1 RbsD_FucU Ribosomal_L7Ae RNase_P_pop3 SpoU_sub_bind TSNR_N

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(93)
Full
(12483)
Representative proteomes UniProt
(55528)
RP15
(1621)
RP35
(6133)
RP55
(12725)
RP75
(21696)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(93)
Full
(12483)
Representative proteomes UniProt
(55528)
RP15
(1621)
RP35
(6133)
RP55
(12725)
RP75
(21696)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(93)
Full
(12483)
Representative proteomes UniProt
(55528)
RP15
(1621)
RP35
(6133)
RP55
(12725)
RP75
(21696)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_742 (release 16.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 93
Number in full: 12483
Average length of the domain: 75.5 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 26.12 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.8 22.8
Trusted cut-off 22.8 22.8
Noise cut-off 22.7 22.7
Model length: 76
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

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 13 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A077ZJQ4 View 3D Structure Click here
A0A0H3GQK6 View 3D Structure Click here
A0A0H3H1M1 View 3D Structure Click here
A0A0H4IRX3 View 3D Structure Click here
A0A175WE81 View 3D Structure Click here
A0A1D8PHA0 View 3D Structure Click here
A0R557 View 3D Structure Click here
A1TG08 View 3D Structure Click here
A1UMF4 View 3D Structure Click here
B2HJ20 View 3D Structure Click here
B4FXA9 View 3D Structure Click here
C0NN95 View 3D Structure Click here
C1H8H0 View 3D Structure Click here
D3ZK81 View 3D Structure Click here
G4VGN4 View 3D Structure Click here
I1KPW8 View 3D Structure Click here
K0EGR1 View 3D Structure Click here
K0ELZ7 View 3D Structure Click here
O25279 View 3D Structure Click here
O51468 View 3D Structure Click here
O94631 View 3D Structure Click here
O96263 View 3D Structure Click here
P0AGJ5 View 3D Structure Click here
P0AGJ6 View 3D Structure Click here
P25270 View 3D Structure Click here
P44703 View 3D Structure Click here
P44906 View 3D Structure Click here
P47494 View 3D Structure Click here
P63177 View 3D Structure Click here
P63179 View 3D Structure Click here
P63180 View 3D Structure Click here
P74261 View 3D Structure Click here
P74328 View 3D Structure Click here
P75424 View 3D Structure Click here
P94538 View 3D Structure Click here
P94978 View 3D Structure Click here
P9WFY5 View 3D Structure Click here
Q06753 View 3D Structure Click here
Q0PBY4 View 3D Structure Click here
Q2FZE0 View 3D Structure Click here