Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
3  structures 430  species 1  interaction 1124  sequences 32  architectures

Family: XendoU (PF09412)

Summary: Endoribonuclease XendoU

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

This is the Wikipedia entry entitled "Endoribonuclease XendoU". More...

Endoribonuclease XendoU Edit Wikipedia article

XendoU
PDB 2c1w EBI.jpg
the structure of xendou: a splicing independent snorna processing endoribonuclease
Identifiers
Symbol XendoU
Pfam PF09412
InterPro IPR018998

In molecular biology, Endoribonuclease XendoU refers to a protein domain. This particular entry represents endoribonucleases involved in RNA biosynthesis which has been named XendoU in Xenopus laevis (African clawed frog). This protein domain belongs to a family of evolutionarily related proteins. XendoU is a U-specific metal dependent enzyme that produces products with a 2'-3' cyclic phosphate termini.

Function

The endonuclease, XendoU, is highly involved in the biosynthesis of a specific subclass of Xenopus laevis encoded small nucleolar RNAs (snoRNA) which are a large family of non-coding RNAs with essential roles in ribosome biogenesis. Most snoRNAs are encoded in introns and are released through the splicing reaction. Others, instead, produced by an alternative pathway consisting of endonucleolytic processing of pre-mRNA. XendoU, is the endoribonuclease responsible for this activity.[1]

Studies have shown that XendoU-RNA complex is Manganese(Mn2+)-independent.This infers that RNA binding and processing activities can be functionally separated since ions are essential for cleavage.[2]

Structure

XendoU is a single-domain protein with roughly globular shape. It contains nine alpha helices and three antiparallel beta sheets; the latter are clustered on one side of the protein.[1]

Homology

XendoU has no homology to any known cellular RNase. However, it has sequence similarity with proteins tentatively annotated as serine proteases.[2]

References

  1. ^ a b Renzi F, Caffarelli E, Laneve P, Bozzoni I, Brunori M, Vallone B (2006). "The structure of the endoribonuclease XendoU: From small nucleolar RNA processing to severe acute respiratory syndrome coronavirus replication.". Proc Natl Acad Sci U S A. 103 (33): 12365–70. PMC 1567885Freely accessible. PMID 16895992. doi:10.1073/pnas.0602426103. 
  2. ^ a b Gioia U, Laneve P, Dlakic M, Arceci M, Bozzoni I, Caffarelli E (2005). "Functional characterization of XendoU, the endoribonuclease involved in small nucleolar RNA biosynthesis.". J Biol Chem. 280 (19): 18996–9002. PMID 15755742. doi:10.1074/jbc.M501160200. 

This article incorporates text from the public domain Pfam and InterPro IPR018998

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Endoribonuclease XendoU Provide feedback

This is a family of endoribonucleases involved in RNA biosynthesis which has been named XendoU in Xenopus laevis. XendoU is a U-specific metal dependent enzyme that produces products with a 2'-3' cyclic phosphate termini.

Literature references

  1. Renzi F, Caffarelli E, Laneve P, Bozzoni I, Brunori M, Vallone B; , Proc Natl Acad Sci U S A. 2006;103:12365-12370.: The structure of the endoribonuclease XendoU: From small nucleolar RNA processing to severe acute respiratory syndrome coronavirus replication. PUBMED:16895992 EPMC:16895992


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018998

This entry represents the EndoU endoribonucleases mostly from eukaryotes. The founding member XendoU is a uridylate-specific, divalent cation-dependent enzyme that produces molecules with 2',3'-cyclic phosphate ends [PUBMED:15755742, PUBMED:16895992]. The human Endou, known as PP11, has endoribonuclease activity with placental tissue specificity [PUBMED:18936097, PUBMED:28610924].

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...

Loading domain graphics...

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(97)
Full
(1124)
Representative proteomes UniProt
(1931)
NCBI
(2187)
Meta
(1)
RP15
(402)
RP35
(687)
RP55
(915)
RP75
(1011)
Jalview View  View  View  View  View  View  View  View  View 
HTML View  View               
PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(97)
Full
(1124)
Representative proteomes UniProt
(1931)
NCBI
(2187)
Meta
(1)
RP15
(402)
RP35
(687)
RP55
(915)
RP75
(1011)
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
(97)
Full
(1124)
Representative proteomes UniProt
(1931)
NCBI
(2187)
Meta
(1)
RP15
(402)
RP35
(687)
RP55
(915)
RP75
(1011)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: pdb_2c1w
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mistry J
Number in seed: 97
Number in full: 1124
Average length of the domain: 224.40 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 67.03 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.1 26.1
Trusted cut-off 26.9 26.1
Noise cut-off 23.9 25.3
Model length: 265
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There is 1 interaction for this family. More...

XendoU

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 XendoU domain has been found. There are 3 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.

Loading structure mapping...