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303  structures 2937  species 0  interactions 10804  sequences 235  architectures

Family: DNA_pol_B (PF00136)

Summary: DNA polymerase family B

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "DNA polymerase". More...

DNA polymerase Edit Wikipedia article

A DNA polymerase is an enzyme that replicates DNA. Such enzymes catalyze the polymerization of dideoxyribonucleotides alongside a DNA strand, which they "read" and use as a template. The newly polymerized molecule is complimentary to the template or antisense strand.

5' to 3' direction

Highly conserved.

DNAPI, DNAPII

holoenzyme. error correction. helicase.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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 Provide feedback

This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.

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 IPR006134

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 ].

The DNA polymerase structure resembles a right hand with fingers, palm, and thumb, with an active site formed by a palm holding the catalytic residues, a thumb that binds the primer:template DNA and fingers interacting with incoming nucleotide, and the N and Exo domains extend from the finger toward the thumb [ PUBMED:7516581 , PUBMED:19718023 , PUBMED:23940661 ].

This domain of DNA polymerase B appears to consist of more than one activities, possibly including elongation, DNA-binding and dNTP binding [ PUBMED:9757117 ].

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 DNA_pol_B-like (CL0194), which has the following description:

DNA polymerases replicate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of a growing chain of DNA. They use a complementary DNA chain as a template.`

The clan contains the following 5 members:

divDNApol DNA_pol_B DNA_pol_B_2 DUF1744 Pox_F12L

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
(29)
Full
(10804)
Representative proteomes UniProt
(37204)
RP15
(2899)
RP35
(5382)
RP55
(8901)
RP75
(12683)
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
(29)
Full
(10804)
Representative proteomes UniProt
(37204)
RP15
(2899)
RP35
(5382)
RP55
(8901)
RP75
(12683)
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
(29)
Full
(10804)
Representative proteomes UniProt
(37204)
RP15
(2899)
RP35
(5382)
RP55
(8901)
RP75
(12683)
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: none
Type: Family
Sequence Ontology: SO:0100021
Author: Sonnhammer ELL
Number in seed: 29
Number in full: 10804
Average length of the domain: 379.6 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 29.3 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.0 23.0
Trusted cut-off 23.0 23.0
Noise cut-off 22.9 22.9
Model length: 459
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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

Selections

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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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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 domain has been found. There are 303 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
A0A044QT95 View 3D Structure Click here
A0A044RLB6 View 3D Structure Click here
A0A044S2R4 View 3D Structure Click here
A0A044SG94 View 3D Structure Click here
A0A077YV06 View 3D Structure Click here
A0A077Z1H5 View 3D Structure Click here
A0A077Z3J7 View 3D Structure Click here
A0A077ZGN5 View 3D Structure Click here
A0A077ZJV4 View 3D Structure Click here
A0A0D2ESJ4 View 3D Structure Click here
A0A0D2FIM0 View 3D Structure Click here
A0A0D2H302 View 3D Structure Click here
A0A0D2H8A6 View 3D Structure Click here
A0A0H3GI42 View 3D Structure Click here
A0A0K0E564 View 3D Structure Click here
A0A0K0E7Y0 View 3D Structure Click here
A0A0K0E894 View 3D Structure Click here
A0A0K0EDG5 View 3D Structure Click here
A0A0K0JMX7 View 3D Structure Click here
A0A0K3AUS7 View 3D Structure Click here
A0A0N4ULP4 View 3D Structure Click here
A0A0R0HLB0 View 3D Structure Click here
A0A0R0KTI8 View 3D Structure Click here
A0A143ZYZ7 View 3D Structure Click here
A0A158Q3E6 View 3D Structure Click here
A0A158Q5H2 View 3D Structure Click here
A0A158Q6N0 View 3D Structure Click here
A0A175VWX8 View 3D Structure Click here
A0A175VZQ5 View 3D Structure Click here
A0A175W5N3 View 3D Structure Click here
A0A1C1CAC2 View 3D Structure Click here
A0A1C1CJ69 View 3D Structure Click here
A0A1C1CR22 View 3D Structure Click here
A0A1C1CRY0 View 3D Structure Click here
A0A1D6H8Z3 View 3D Structure Click here
A0A1D6INH0 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