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.
335  structures 2751  species 0  interactions 9980  sequences 201  architectures

Family: DNA_pol_B_exo1 (PF03104)

Summary: DNA polymerase family B, exonuclease domain

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.

DNA polymerase family B, exonuclease domain Provide feedback

This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.

Literature references

  1. Wang J, Yu P, Lin TC, Konigsberg WH, Steitz TA; , Biochemistry 1996;35:8110-8119.: Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions. PUBMED:8679562 EPMC:8679562

  2. Zhou M, Mao C, Rodriguez AC, Kiefer JR, Kucera RB, Beese LS; , Acta Crystallogr D Biol Crystallogr 1998;54:994-995.: Crystallization and preliminary diffraction analysis of a hyperthermostable DNA polymerase from a Thermococcus archaeon. PUBMED:9757117 EPMC:9757117


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006133

DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases EC ) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [ PUBMED:8679562 ], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate [ PUBMED:9757117 ].

This domain is the exonuclease domain of family B DNA polymerases. It adopts a ribonuclease H type fold [ PUBMED:8679562 ].

Domain organisation

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

Loading domain graphics...

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...

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
(32)
Full
(9980)
Representative proteomes UniProt
(30063)
RP15
(2421)
RP35
(4900)
RP55
(8281)
RP75
(11786)
Jalview View  View  View  View  View  View  View 
HTML View             
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
(32)
Full
(9980)
Representative proteomes UniProt
(30063)
RP15
(2421)
RP35
(4900)
RP55
(8281)
RP75
(11786)
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
(32)
Full
(9980)
Representative proteomes UniProt
(30063)
RP15
(2421)
RP35
(4900)
RP55
(8281)
RP75
(11786)
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: Prosite
Previous IDs: DNA_pol_B_exo;
Type: Family
Sequence Ontology: SO:0100021
Author: Sonnhammer ELL , Griffiths-Jones SR
Number in seed: 32
Number in full: 9980
Average length of the domain: 273.70 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 22.14 %

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 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 337
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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 DNA_pol_B_exo1 domain has been found. There are 335 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.

Loading structure mapping...

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
A0A0K3AUS7 View 3D Structure Click here
A0A0K3AUS7 View 3D Structure Click here
A0A0P0VJF5 View 3D Structure Click here
A0A0R0HLB0 View 3D Structure Click here
A0A0R0KTI8 View 3D Structure Click here
A0A0R0KTI8 View 3D Structure Click here
A0A1D6H8Z3 View 3D Structure Click here
A0A1D6INH0 View 3D Structure Click here
A0A1D6INH0 View 3D Structure Click here
A0A1D6MVL6 View 3D Structure Click here
A0A1D6N6A8 View 3D Structure Click here
A0A1D6QLT8 View 3D Structure Click here
A0A1D8PK28 View 3D Structure Click here
A0A1D8PKE9 View 3D Structure Click here
A0A1D8PKE9 View 3D Structure Click here
A0A1D8PR64 View 3D Structure Click here
A0A1D8PTD0 View 3D Structure Click here
A4HX52 View 3D Structure Click here
A4I965 View 3D Structure Click here
A4IBX6 View 3D Structure Click here
B0V351 View 3D Structure Click here
B3DKJ9 View 3D Structure Click here
C7IVS4 View 3D Structure Click here
D3Z8X4 View 3D Structure Click here
E7FB68 View 3D Structure Click here
F4HW04 View 3D Structure Click here
F4IFN6 View 3D Structure Click here
I1KBL4 View 3D Structure Click here
I1LRE2 View 3D Structure Click here
K7K4M3 View 3D Structure Click here
K7K8U8 View 3D Structure Click here
K7KLF0 View 3D Structure Click here
O48653 View 3D Structure Click here
O48901 View 3D Structure Click here
O54747 View 3D Structure Click here
O62218 View 3D Structure Click here
O89042 View 3D Structure Click here
P09884 View 3D Structure Click here
P13382 View 3D Structure Click here
P14284 View 3D Structure Click here
P14284 View 3D Structure Click here
P15436 View 3D Structure Click here
P21189 View 3D Structure Click here
P21189 View 3D Structure Click here
P21951 View 3D Structure Click here
P26019 View 3D Structure Click here
P28040 View 3D Structure Click here
P28340 View 3D Structure Click here
P30316 View 3D Structure Click here
P33609 View 3D Structure Click here
P52431 View 3D Structure Click here
P54358 View 3D Structure Click here
P87154 View 3D Structure Click here
P90829 View 3D Structure Click here
Q07864 View 3D Structure Click here
Q4CUY9 View 3D Structure Click here
Q4D2H0 View 3D Structure Click here
Q4D440 View 3D Structure Click here
Q4DT90 View 3D Structure Click here
Q4DUF0 View 3D Structure Click here
Q54N97 View 3D Structure Click here
Q54RD4 View 3D Structure Click here
Q54SV8 View 3D Structure Click here
Q58295 View 3D Structure Click here
Q766Z3 View 3D Structure Click here
Q766Z3 View 3D Structure Click here
Q7KQL4 View 3D Structure Click here
Q9FHA3 View 3D Structure Click here
Q9GSR1 View 3D Structure Click here
Q9GSR1 View 3D Structure Click here
Q9LRE6 View 3D Structure Click here
Q9LVN7 View 3D Structure Click here
Q9P6L6 View 3D Structure Click here
Q9P6L6 View 3D Structure Click here
Q9VCN1 View 3D Structure Click here
Q9WVF7 View 3D Structure Click here