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32  structures 3529  species 2  interactions 6914  sequences 92  architectures

Family: DNA_pol_A_exo1 (PF01612)

Summary: 3'-5' exonuclease

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3'-5' exonuclease Provide feedback

This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction [4,5]. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein [3]. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.

Literature references

  1. Ollis DL, Brick P, Hamlin R, Xuong NG, Steitz TA; , Nature 1985;313:762-766.: Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. PUBMED:3883192 EPMC:3883192

  2. Moser MJ, Holley WR, Chatterjee A, Mian IS; , Nucleic Acids Res 1997;25:5110-5118.: The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains. PUBMED:9396823 EPMC:9396823

  3. Yan H, Chen CY, Kobayashi R, Newport J; , Nat Genet 1998;19:375-378.: Replication focus-forming activity 1 and the Werner syndrome gene product PUBMED:9697700 EPMC:9697700

  4. Gray MD, Shen JC, Kamath-Loeb AS, Blank A, Sopher BL, Martin GM, Oshima J, Loeb LA; , Nat Genet 1997;17:100-103.: The Werner syndrome protein is a DNA helicase. PUBMED:9288107 EPMC:9288107

  5. Suzuki N, Shimamoto A, Imamura O, Kuromitsu J, Kitao S, Goto M, Furuichi Y; , Nucleic Acids Res 1997;25:2973-2978.: DNA helicase activity in Werner's syndrome gene product synthesized in a baculovirus system. PUBMED:9224595 EPMC:9224595


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002562

This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [PUBMED:9697700].

Gene Ontology

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Domain organisation

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

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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
(27)
Full
(6914)
Representative proteomes NCBI
(6043)
Meta
(5677)
RP15
(797)
RP35
(1441)
RP55
(1966)
RP75
(2350)
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Format an alignment

  Seed
(27)
Full
(6914)
Representative proteomes NCBI
(6043)
Meta
(5677)
RP15
(797)
RP35
(1441)
RP55
(1966)
RP75
(2350)
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
(27)
Full
(6914)
Representative proteomes NCBI
(6043)
Meta
(5677)
RP15
(797)
RP35
(1441)
RP55
(1966)
RP75
(2350)
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.

Pfam alignments:

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_659 (release 4.1)
Previous IDs: 3_5_exonuclease; 3_5_exonuc;
Type: Domain
Author: Bashton M, Bateman A, Griffiths-Jones SR
Number in seed: 27
Number in full: 6914
Average length of the domain: 173.20 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 27.78 %

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 20.4 20.4
Trusted cut-off 20.4 20.4
Noise cut-off 20.3 20.3
Model length: 176
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

DNA_pol_A HRDC

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 DNA_pol_A_exo1 domain has been found. There are 32 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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