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75  structures 7177  species 0  interactions 19708  sequences 311  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


Internal database links

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 ].

Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction [ PUBMED:9288107 , PUBMED:9224595 ]. 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 [ PUBMED:9697700 ]. 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.

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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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 and the UniProtKB sequence database. More...

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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
(24)
Full
(19708)
Representative proteomes UniProt
(71655)
RP15
(3605)
RP35
(9874)
RP55
(18311)
RP75
(28531)
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PP/heatmap 1            

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

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

Format an alignment

  Seed
(24)
Full
(19708)
Representative proteomes UniProt
(71655)
RP15
(3605)
RP35
(9874)
RP55
(18311)
RP75
(28531)
Alignment:
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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
(24)
Full
(19708)
Representative proteomes UniProt
(71655)
RP15
(3605)
RP35
(9874)
RP55
(18311)
RP75
(28531)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Pfam-B_659 (release 4.1)
Previous IDs: 3_5_exonuclease; 3_5_exonuc;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bashton M , Bateman A , Griffiths-Jones SR
Number in seed: 24
Number in full: 19708
Average length of the domain: 173.40 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 28.29 %

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 23.2 23.2
Trusted cut-off 23.2 23.2
Noise cut-off 23.1 23.1
Model length: 176
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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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 75 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0N7KDQ1 View 3D Structure Click here
A0A0N7KNI7 View 3D Structure Click here
A0A0P0V4C6 View 3D Structure Click here
A0A0P0V657 View 3D Structure Click here
A0A0P0X1K0 View 3D Structure Click here
A0A0P0X1X7 View 3D Structure Click here
A0A0P0XUY4 View 3D Structure Click here
A0A0R0EHN9 View 3D Structure Click here
A0A0R0F1Q1 View 3D Structure Click here
A0A0R0FA00 View 3D Structure Click here
A0A0R0GNL3 View 3D Structure Click here
A0A0R0H3J5 View 3D Structure Click here
A0A0R0HM63 View 3D Structure Click here
A0A0R0IV41 View 3D Structure Click here
A0A0R0J373 View 3D Structure Click here
A0A0R0JXJ9 View 3D Structure Click here
A0A0R0KA28 View 3D Structure Click here
A0A0R4IHR6 View 3D Structure Click here
A0A1D6EMH1 View 3D Structure Click here
A0A1D6FNL8 View 3D Structure Click here
A0A1D6FP71 View 3D Structure Click here
A0A1D6G0W4 View 3D Structure Click here
A0A1D6GBH8 View 3D Structure Click here
A0A1D6HR85 View 3D Structure Click here
A0A1D6ICX7 View 3D Structure Click here
A0A1D6IJ41 View 3D Structure Click here
A0A1D6IZ69 View 3D Structure Click here
A0A1D6JFD6 View 3D Structure Click here
A0A1D6JP11 View 3D Structure Click here
A0A1D6KJQ6 View 3D Structure Click here
A0A1D6KUQ4 View 3D Structure Click here
A0A1D6L680 View 3D Structure Click here
A0A1D6NGT3 View 3D Structure Click here
A0A1D6NJW0 View 3D Structure Click here
A0A1D6P140 View 3D Structure Click here
A0A1D8PDF4 View 3D Structure Click here
A0A1P8BGD5 View 3D Structure Click here
A0A2R8QQ92 View 3D Structure Click here
A0A2R8QSS0 View 3D Structure Click here
A0A381MTM9 View 3D Structure Click here
A0A5K1K919 View 3D Structure Click here
A0A5K1K919 View 3D Structure Click here
A3BFX5 View 3D Structure Click here
A4I774 View 3D Structure Click here
A4I804 View 3D Structure Click here
A4I9T6 View 3D Structure Click here
A4IBI7 View 3D Structure Click here
A9LLI7 View 3D Structure Click here
A9LLI8 View 3D Structure Click here
B2GUW4 View 3D Structure Click here
B4FDY5 View 3D Structure Click here
B4FTF6 View 3D Structure Click here
B4FTR6 View 3D Structure Click here
B6TGX6 View 3D Structure Click here
C6T412 View 3D Structure Click here
D4A1X2 View 3D Structure Click here
D4AD21 View 3D Structure Click here
E7EY45 View 3D Structure Click here
F1LTH9 View 3D Structure Click here
F1Q5Q7 View 3D Structure Click here
F1QBW6 View 3D Structure Click here
F4I526 View 3D Structure Click here
F4I6M1 View 3D Structure Click here
F4ITJ6 View 3D Structure Click here
G5EBX6 View 3D Structure Click here
I1JJ76 View 3D Structure Click here
I1KFD3 View 3D Structure Click here
I1KK93 View 3D Structure Click here
I1LB63 View 3D Structure Click here
I1LW83 View 3D Structure Click here
I1M8Y6 View 3D Structure Click here
I1MGC8 View 3D Structure Click here
I1MW66 View 3D Structure Click here
I1MXE5 View 3D Structure Click here
I1MYA3 View 3D Structure Click here
I6XF17 View 3D Structure Click here
K7KIZ6 View 3D Structure Click here
K7KNU4 View 3D Structure Click here
K7M4K7 View 3D Structure Click here
K7MTD2 View 3D Structure Click here
K7MTD3 View 3D Structure Click here
K7MXW4 View 3D Structure Click here
K7N1B8 View 3D Structure Click here
K7N5C5 View 3D Structure Click here
K7UW05 View 3D Structure Click here
O09053 View 3D Structure Click here
O96144 View 3D Structure Click here
P00582 View 3D Structure Click here
P09155 View 3D Structure Click here
P34603 View 3D Structure Click here
P34607 View 3D Structure Click here
P56960 View 3D Structure Click here
Q01780 View 3D Structure Click here
Q0D6Q9 View 3D Structure Click here
Q0JNE9 View 3D Structure Click here
Q0P3U3 View 3D Structure Click here
Q0WVE8 View 3D Structure Click here
Q10146 View 3D Structure Click here
Q10RJ0 View 3D Structure Click here
Q12149 View 3D Structure Click here
Q14191 View 3D Structure Click here
Q17902 View 3D Structure Click here
Q21251 View 3D Structure Click here
Q4CSB5 View 3D Structure Click here
Q4D7B2 View 3D Structure Click here
Q4D7Z7 View 3D Structure Click here
Q4DSE3 View 3D Structure Click here
Q4DVP5 View 3D Structure Click here
Q54MU3 View 3D Structure Click here
Q54SM0 View 3D Structure Click here
Q54YU4 View 3D Structure Click here
Q54YU5 View 3D Structure Click here
Q55AW0 View 3D Structure Click here
Q5JND6 View 3D Structure Click here
Q5SMR6 View 3D Structure Click here
Q5W6Y1 View 3D Structure Click here
Q6Z4T3 View 3D Structure Click here
Q6Z4T5 View 3D Structure Click here
Q7XP25 View 3D Structure Click here
Q7XWZ1 View 3D Structure Click here
Q84LH3 View 3D Structure Click here
Q84ND9 View 3D Structure Click here
Q8CDF7 View 3D Structure Click here
Q8I282 View 3D Structure Click here
Q8I7W9 View 3D Structure Click here
Q8IB75 View 3D Structure Click here
Q8ILY1 View 3D Structure Click here
Q8N9H8 View 3D Structure Click here
Q8NHP7 View 3D Structure Click here
Q8VEG4 View 3D Structure Click here
Q93VU9 View 3D Structure Click here
Q9NA69 View 3D Structure Click here
Q9NA69 View 3D Structure Click here
Q9NVH0 View 3D Structure Click here
Q9SIH3 View 3D Structure Click here
Q9VE86 View 3D Structure Click here
Q9VFF3 View 3D Structure Click here
Q9VGN7 View 3D Structure Click here
Q9VIF1 View 3D Structure Click here
Q9W1K4 View 3D Structure Click here
Q9XUL8 View 3D Structure Click here