Summary: DNA polymerase family B, exonuclease domain
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DNA polymerase family B, exonuclease domain Provide feedback
This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.
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
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
|Similarity to PfamA using HHSearch:||DNA_pol_B_exo2 RNase_H_2|
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 has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [PUBMED:8679562].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||DNA-directed DNA polymerase activity (GO:0003887)|
|Biological process||DNA replication (GO:0006260)|
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Curation and family details
|Author:||Sonnhammer ELL, Griffiths-Jones SR|
|Number in seed:||32|
|Number in full:||3652|
|Average length of the domain:||275.30 aa|
|Average identity of full alignment:||17 %|
|Average coverage of the sequence by the domain:||26.07 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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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 166 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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