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.
10  structures 311  species 0  interactions 896  sequences 24  architectures

Family: XRN_N (PF03159)

Summary: XRN 5'-3' exonuclease N-terminus

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

XRN 5'-3' exonuclease N-terminus Provide feedback

This family aligns residues towards the N-terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity EC:3.1.11.-. Thus, the aligned region may be necessary for 5' to 3' exonuclease function. The family also contains several Xrn1 and Xrn2 proteins. The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalysing cytoplasmic mRNA degradation in multiple decay pathways, whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus [3].

Literature references

  1. Szankasi P, Smith GR; , Curr Genet 1996;30:284-293.: Requirement of S. pombe exonuclease II, a homologue of S. cerevisiae Sep1, for normal mitotic growth and viability. PUBMED:8781170 EPMC:8781170

  2. Till DD, Linz B, Seago JE, Elgar SJ, Marujo PE, Elias ML, Arraiano CM, McClellan JA, McCarthy JE, Newbury SF; , Mech Dev 1998;79:51-55.: Identification and developmental expression of a 5'-3' exoribonuclease from Drosophila melanogaster. PUBMED:10349620 EPMC:10349620

  3. Kastenmayer JP, Green PJ; , Proc Natl Acad Sci U S A 2000;97:13985-13990.: Novel features of the XRN-family in Arabidopsis: evidence that AtXRN4, one of several orthologs of nuclear Xrn2p/Rat1p, functions in the cytoplasm. PUBMED:11106401 EPMC:11106401


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004859

Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.

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...

Pfam Clan

This family is a member of clan PIN (CL0280), which has the following description:

This superfamily contains a variety of nuclease enzymes, including PIN domains and the FLAP exonucleases.

The clan contains the following 16 members:

5_3_exonuc_N DUF188 DUF4411 Fcf1 Mut7-C NYN NYN_YacP PIN PIN_2 PIN_3 PIN_4 RNase_Zc3h12a RNase_Zc3h12a_2 UPF0278 XPG_N XRN_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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(17)
Full
(896)
Representative proteomes NCBI
(928)
Meta
(242)
RP15
(247)
RP35
(365)
RP55
(514)
RP75
(593)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(17)
Full
(896)
Representative proteomes NCBI
(928)
Meta
(242)
RP15
(247)
RP35
(365)
RP55
(514)
RP75
(593)
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
(17)
Full
(896)
Representative proteomes NCBI
(928)
Meta
(242)
RP15
(247)
RP35
(365)
RP55
(514)
RP75
(593)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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_2349 (release 6.5)
Previous IDs: DUF251;
Type: Family
Author: Mifsud W, Moxon SJ
Number in seed: 17
Number in full: 896
Average length of the domain: 207.90 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 22.33 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.9 22.9
Trusted cut-off 24.0 23.1
Noise cut-off 22.8 21.5
Model length: 237
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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.

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 XRN_N domain has been found. There are 10 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.

Loading structure mapping...