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38  structures 7380  species 0  interactions 10841  sequences 55  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 27 members:

5_3_exonuc_N DUF1308 DUF188 DUF4411 DUF5615 DUF5616 Fcf1 Mut7-C NYN NYN_YacP PIN PIN7 PIN_10 PIN_11 PIN_12 PIN_2 PIN_3 PIN_4 PIN_5 PIN_6 PIN_8 PIN_9 PRORP RNase_Zc3h12a RNase_Zc3h12a_2 XPG_N XRN_N


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...

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Representative proteomes UniProt

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

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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.

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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
Sequence Ontology: SO:0000417
Author: Bateman A , Griffiths-Jones SR
Number in seed: 718
Number in full: 10841
Average length of the domain: 167.50 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 23.23 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 34.3 34.3
Trusted cut-off 34.3 34.3
Noise cut-off 34.1 34.2
Model length: 159
Family (HMM) version: 18
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


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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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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 38 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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