Summary: DNA polymerase family B
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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.
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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
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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
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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
SCOOP: | divDNApol DNA_pol_B_2 DUF1744 |
External database links
HOMSTRAD: | DNA_pol_B |
PROSITE: | PDOC00107 |
SCOP: | 1noy |
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.
Molecular function | DNA binding (GO:0003677) |
nucleotide binding (GO:0000166) |
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_F12LAlignments
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 (29) |
Full (10804) |
Representative proteomes | UniProt (37204) |
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RP15 (2899) |
RP35 (5382) |
RP55 (8901) |
RP75 (12683) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (29) |
Full (10804) |
Representative proteomes | UniProt (37204) |
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RP15 (2899) |
RP35 (5382) |
RP55 (8901) |
RP75 (12683) |
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Raw Stockholm | |||||||
Gzipped |
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
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
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 459 | ||||||||||||
Family (HMM) version: | 24 | ||||||||||||
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_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.