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17  structures 4577  species 4  interactions 6210  sequences 20  architectures

Family: 5_3_exonuc_N (PF02739)

Summary: 5'-3' exonuclease, N-terminal resolvase-like domain

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5'-3' exonuclease, N-terminal resolvase-like domain Provide feedback

No Pfam abstract.

Literature references

  1. Eom SH, Wang J, Steitz TA; , Nature 1996;382:278-281.: Structure of Taq ploymerase with DNA at the polymerase active site. PUBMED:8717047 EPMC:8717047

  2. Ceska TA, Sayers JR, Stier G, Suck D; , Nature 1996;382:90-93.: A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease. PUBMED:8657312 EPMC:8657312


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020046

The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [PUBMED:7926735, PUBMED:10322433, PUBMED:8464724]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families.

In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures.

This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [PUBMED:8717047, PUBMED:8657312].

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 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
(25)
Full
(6210)
Representative proteomes NCBI
(4680)
Meta
(3819)
RP15
(413)
RP35
(828)
RP55
(1081)
RP75
(1278)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(25)
Full
(6210)
Representative proteomes NCBI
(4680)
Meta
(3819)
RP15
(413)
RP35
(828)
RP55
(1081)
RP75
(1278)
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
(25)
Full
(6210)
Representative proteomes NCBI
(4680)
Meta
(3819)
RP15
(413)
RP35
(828)
RP55
(1081)
RP75
(1278)
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_716 (release 3.0)
Previous IDs: none
Type: Domain
Author: Bateman A, Griffiths-Jones SR
Number in seed: 25
Number in full: 6210
Average length of the domain: 164.00 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 23.04 %

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 22.1 22.1
Trusted cut-off 22.1 22.1
Noise cut-off 21.9 22.0
Model length: 169
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There are 4 interactions for this family. More...

5_3_exonuc Taq-exonuc DNA_pol_A RNaseH_C

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 5_3_exonuc_N domain has been found. There are 17 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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