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UniProtKB - P03680 (DPOL_BPPH2)

Entry version 127 (16 Oct 2019)
Sequence version 1 (21 Jul 1986)
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Protein

DNA polymerase

Gene

2

Organism
Bacillus phage phi29 (Bacteriophage phi-29)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Polymerase responsible for protein-primed viral DNA replication by strand displacement with high processivity and fidelity (PubMed:3863101) (PubMed:2498321). To start replication, the DNA polymerase forms a heterodimer with a free primer terminal protein (TP), recognizes the replication origins at both 5' ends of the linear chromosome, and initiates replication using as primer the OH-group of Ser-232 of the TP (PubMed:22210885). This polymerase possesses three enzymatic activities: DNA synthesis (polymerase), primer terminal protein (TP) deoxynucleotidylation, which is the formation of a covalent linkage (phosphoester) between the hydroxyl group of a specific serine residue in TP and 5'-dAMP, a reaction directed by the second T at the 3' end, and 3' to 5' exonuclease activity (PubMed:2790959). Exonuclease activity has a proofreading purpose (PubMed:2790959). DNA polymerase edits the polymerization errors using an intramolecular pathway as the primer terminus travels from one active site to the other without dissociation from the DNA (PubMed:10493855). DNA polymerization catalyzed by the DNA polymerase is a highly accurate process, but the protein-primed initiation is a quite inaccurate reaction (PubMed:8428945). Since the polymerase initiates the replication on the second thymine, the TP-dAMP initiation product translocates backwards to recover the template information of the first nucleotide (sliding back-mechanism) (PubMed:19011105).9 Publications

Miscellaneous

This DNA polymerase requires a protein as a primer.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+4 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei12Essential for 3'-5' exonucleolysis2 Publications1
Sitei14Essential for 3'-5' exonucleolysis2 Publications1
Sitei15Involved in proofreading function by stabilization of the frayed primer-terminus at the 3'-5' exonuclease active site1 Publication1
Sitei62Involved in proofreading function by stabilization of the frayed primer-terminus at the 3'-5' exonuclease active site1 Publication1
Sitei65Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication1
Sitei66Essential for 3'-5' exonucleolysis2 Publications1
Sitei93Involved in binding template-primer structures1 Publication1
Sitei122Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication1
Sitei123Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi145Magnesium 1Combined sources1
Sitei148Involved in the stabilization of the frayed 3' terminus at the exonuclease active site1 Publication1
Metal bindingi169Magnesium 1Combined sources1
Metal bindingi249Magnesium 2; catalyticCombined sources1 Publication1
Metal bindingi250Magnesium 2; via carbonyl oxygen; catalyticCombined sources1 Publication1
Sitei252Probably involved in binding template-primer structures1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei254TTP; via amide nitrogenCombined sources1
Sitei254Probably involved in nucleotide binding selection1 Publication1
Sitei356Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication1
Sitei364Involved in the binding of DNA and dNTP1 Publication1
Sitei366Stabilization of the incoming nucleotide1 Publication1
Binding sitei371TTPCombined sources1
Sitei371Interacts with the phosphate groups of the incoming nucleotide1 Publication1
Sitei379Stabilization of the incoming nucleotide1 Publication1
Binding sitei383TTPCombined sources1
Sitei383Probably involved in nucleotide binding selection1 Publication1
Sitei384Probably involved in positioning the templating nucleotide at the polymerization active site and in controlling nucleotide insertion fidelity1 Publication1
Sitei387Probably involved in binding template-primer structures1 Publication1
Sitei390Probably involved in nucleotide binding selection1 Publication1
Sitei391Probably involved in binding template-primer structures1 Publication1
Sitei420Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication1
Sitei434Probably involved in binding template-primer structures1 Publication1
Sitei438Probably involved in binding template-primer structures1 Publication1
Metal bindingi456Magnesium 2; catalytic1 Publication1
Metal bindingi458Magnesium 2; catalyticCombined sources1
Binding sitei458TTPCombined sources1
Sitei498Probably involved in binding template-primer structures1 Publication1
Sitei500Probably involved in binding template-primer structures1 Publication1
Sitei529Stabilizes the primer-terminus at the polymerization active site and contributes to the coordination between the exonuclease and polymerazation activities1 Publication1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionDNA-binding, DNA-directed DNA polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase
Biological processDNA replication, Viral DNA replication
LigandMagnesium, Metal-binding, Nucleotide-binding

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
DNA polymerase (EC:2.7.7.71 Publication, EC:3.1.11.-1 Publication)
Alternative name(s):
Gene product 2Curated
Short name:
gp2Curated
Protein p2Curated
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:2
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiBacillus phage phi29 (Bacteriophage phi-29)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri10756 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiViruses › Caudovirales › Podoviridae › Picovirinae › Salasvirus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section only exists in viral entries and indicates the host(s) either as a specific organism or taxonomic group of organisms that are susceptible to be infected by a virus.<p><a href='/help/virus_host' target='_top'>More...</a></p>Virus hostiBacillus subtilis [TaxID: 1423]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000001207 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Genome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi12D → A: Strong loss of 3'-5' exonucleolysis. 2 Publications1
Mutagenesisi14E → A: Strong loss of 3'-5' exonucleolysis. 2 Publications1
Mutagenesisi15T → I: 95% loss of ssDNA-binding. Decreased in fidelity of DNA replication. 1 Publication1
Mutagenesisi59Y → F: Almost no effect on replication activity. About 20% loss of TP-DNA initiation, 20% loss of TP-DNA replication and 10% loss of TP-DNA amplification. Complete loss of interaction with TP. 1 Publication1
Mutagenesisi59Y → L: 3 fold decrease in replication activity. About 80% loss of TP-DNA initiation, 70% loss of TP-DNA replication and 97% loss of TP-DNA amplification. Complete loss of interaction with TP. 1 Publication1
Mutagenesisi59Y → R: 3 fold decrease in replication activity. About 75% loss of TP-DNA initiation, complete loss of TP-DNA replication and complete loss of TP-DNA amplification. 1 Publication1
Mutagenesisi61H → L: 5 fold decrease in replication activity. About 85% loss of TP-DNA initiation, 80% loss of TP-DNA replication and complete loss of TP-DNA amplification. Complete loss of interaction with TP. 1 Publication1
Mutagenesisi61H → R: 100 fold decrease in replication activity. Complete loss of interaction with TP. 1 Publication1
Mutagenesisi62N → D or H: 88% loss of ssDNA-binding. Decreased in fidelity of DNA replication. 1 Publication1
Mutagenesisi65F → S: Loss of capacity to interact with a DNA primer/template structure. 1 Publication1
Mutagenesisi66D → A: Strong loss of 3'-5' exonucleolysis. 2 Publications1
Mutagenesisi69F → S: 2 fold decrease in replication activity. About 50% loss of TP-DNA initiation, 40% loss of TP-DNA replication and 60% loss of TP-DNA amplification. Complete loss of interaction with TP. 1 Publication1
Mutagenesisi69F → Y: 2 fold decrease in replication activity. About 80% loss of TP-DNA initiation, 50% loss of TP-DNA replication and almost 95% loss of TP-DNA. Complete loss of interaction with TP amplification. 1 Publication1
Mutagenesisi122S → T: Loss of capacity to interact with a DNA primer/template structure. 1 Publication1
Mutagenesisi123L → N: Loss of capacity to interact with a DNA primer/template structure. 1 Publication1
Mutagenesisi128F → A: Slight loss of interaction with TP. 1 Publication1
Mutagenesisi128F → Y: Almost complete loss of interaction with TP. 1 Publication1
Mutagenesisi143K → I or R: Strong loss of 3'-5' exonuclease, proofreading and strand-displacement activities. 1 Publication1
Mutagenesisi148Y → A: Reduced capacity to stabilize the binding of the primer terminus at the 3'-5' exonuclease active site. 1 Publication1
Mutagenesisi169D → A: Strong loss of 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi187R → K: No effect on DNA-binding, TP binding and replication/amplification. 1 Publication1
Mutagenesisi189T → A: No effect on DNA-binding, TP binding and replication/amplification. 1 Publication1
Mutagenesisi192S → I: Loss of DNA-binding. Reduced TP binding. 25% loss of replication and almost complete loss of amplification. 1 Publication1
Mutagenesisi192S → N: Loss of DNA-binding. No effect on TP binding. 50% loss of replication/amplification. 1 Publication1
Mutagenesisi196K → I: Loss of DNA-binding. Reduced TP binding. 25% loss of replication and almost complete loss of amplification. 6-fold reduced 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi196K → R: Slight loss of DNA-binding. No loss of replication and amplification. 1 Publication1
Mutagenesisi198F → V: Loss of DNA-binding. Reduced TP binding. 25% loss of replication and almost complete loss of amplification. 6-fold reduced 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi206K → I: No effect on DNA-binding. Reduced TP binding. 70% loss of replication and 20% loss of amplification. 1 Publication1
Mutagenesisi223R → I: Favored exonucleolysis (low pol/exo ratio). 2 Publications1
Mutagenesisi226Y → F: Favored polymerization (high pol/exo ratio). decrease in forward and reverse rates of translocation. Increased affinity for dNTP and for pyrophosphate in the pre-translocation state. 3 Publications1
Mutagenesisi226Y → S: Favored exonucleolysis. Complete loss of polymerization. 2 Publications1
Mutagenesisi227R → I: Favored exonucleolysis (low pol/exo ratio). 2 Publications1
Mutagenesisi227R → K: No effect on the pol/exo ratio. 1 Publication1
Mutagenesisi228G → A: Favored polymerization (high pol/exo ratio). 2 Publications1
Mutagenesisi229G → A: Favored exonucleolysis (low pol/exo ratio). 2 Publications1
Mutagenesisi229G → D: Favored exonucleolysis. Complete loss of polymerization. 2 Publications1
Mutagenesisi230F → A: Favored polymerization (high pol/exo ratio). 2 Publications1
Mutagenesisi230F → S: Favored exonucleolysis (low pol/exo ratio). 2 Publications1
Mutagenesisi230F → Y: No effect on the pol/exo ratio. 1 Publication1
Mutagenesisi249D → E: Complete loss of DNA polymerase activity. Slight decrease in template-primer binding. No effect on 3' to 5' exonucleolysis. 1 Publication1
Mutagenesisi250V → A: No effect on TP-DNA replication. 1 Publication1
Mutagenesisi250V → F: Complete loss of TP-DNA replication. 1 Publication1
Mutagenesisi251N → D: No effect on TP-DNA replication. 1 Publication1
Mutagenesisi252S → G: 40% loss of DNA polymerase activity. No effect on translocation or stabilization of the incorporated nucIeotide. No effect on 3' to 5' exonucleolysis. 1 Publication1
Mutagenesisi252S → R: Complete loss of DNA polymerase activity. Drastic loss of template-primer binding. No effect on 3' to 5' exonucleolysis and interaction with the TP primer. 1 Publication1
Mutagenesisi253L → V: 30% loss of DNA polymerase activity. No effect on translocation or stabilization of the incorporated nucIeotide. No effect on 3' to 5' exonucleolysis. 1 Publication1
Mutagenesisi254Y → F: Decreased dNTP binding affinity. 10-fold reduced affinity for the correct nucleotide. 1 Publication1
Mutagenesisi254Y → V: Loss of discrimination for rNTPs over dNTPs. 1 Publication1
Mutagenesisi255P → S: 30% loss of DNA polymerase activity. No effect on translocation or stabilization of the incorporated nucIeotide. No effect on 3' to 5' exonucleolysis. 1 Publication1
Mutagenesisi364I → Q: Partial loss of hability to stably bind the DNA substrate. 1 Publication1
Mutagenesisi364I → R: Complete loss of hability to stably bind the DNA substrate. 1 Publication1
Mutagenesisi366K → T: Slight decrease in DNA-binding capacity. No effect on polymerisation activity, except that it is reduced in the absence of a DNA template. Reduced affinity for the initiating nucleotide. 3 fold reduction of the initiation activity in the presence of p6. 1 Publication1
Mutagenesisi371K → T: Strong decrease in the affinity for dNTPs and pyrophosphorolytic activity. No effect on exonucleolysis. 1 Publication1
Mutagenesisi379K → T: Slight increase in DNA-binding capacity. Reduced affinity for the initiating nucleotide. 1 Publication1
Mutagenesisi383K → P: Complete loss of incorporation of dNTP substrates using either DNA or TP as primer. No effect on 3' to 5' exonucleolysis. 1 Publication1
Mutagenesisi383K → R: Strong loss of ability to use dNTPs in both processive and non-processive DNA synthesis. Impaired progression from protein-primed initiation to DNA elongation. No effect on 3' to 5' exonucleolysis. 1 Publication1
Mutagenesisi384L → R: Reduced nucleotide insertion fidelity during DNA-primed polymerization and protein-primed initiation. No effect on the affinity for the different dNTPs. 1 Publication1
Mutagenesisi387N → Y: 3-fold higher Km value for dATP and more than 11-fold lower Vmax value than the wild-type enzyme in the initiation reaction. Impaired in enzyme-DNA translocation. 1 Publication1
Mutagenesisi388S → G: No effect on initiation and polymerization activities. Increased efficiency of dNTP incorporation in non-templated reactions. 1 Publication1
Mutagenesisi390Y → F: Decreased dNTP binding affinity in the post-translocation state. 4.6-fold reduced affinity for the correct nucleotide. 2 Publications1
Mutagenesisi390Y → S: Decreased dNTP binding affinity. 14-fold reduced affinity for the correct nucleotide. Loss of discrimination against dA insertion opposite 8oxodG. 2 Publications1
Mutagenesisi391G → D: Complete loss of template-primer binding. 1 Publication1
Mutagenesisi392K → Q: 50% loss of exonuclease activity. 80% loss of processivity. No effect on DNA polymerase/DNA complex formation. 1 Publication1
Mutagenesisi392K → R: 90% loss of exonuclease activity. 80% loss of processivity. No effect on DNA polymerase/DNA complex formation. 1 Publication1
Mutagenesisi393F → Y: Severe decrease in initial binding to template-primer DNA molecules. 1 Publication1
Mutagenesisi434T → N: Complete loss of TP-dAMP formation. Almost complete loss of DNA polymerization. 1 Publication1
Mutagenesisi437A → G: No effect on TP-dAMP formation. 20% loss of DNA polymerization. 1 Publication1
Mutagenesisi438R → I: Complete loss of TP-dAMP formation. Almost complete loss of DNA polymerization. 1 Publication1
Mutagenesisi438R → K: Complete loss of TP-dAMP formation. 30% loss of DNA polymerization. 1 Publication1
Mutagenesisi454Y → F: No effect on the formation of the covalent complex between the TP and 5'-dAMP. Loss of replication of a p3-DNA complex or a primed M13 DNA. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi455C → G: 65% loss of formation of the covalent complex between the TP and 5'-dAMP. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi456D → G: 50% loss of synthetic activities, TP-primed initiation and DNA-primed polymerization. When polymerization requires an efficient translocation along the template, catalytic efficiency is strongly reduced. 90% loss of formation of the covalent complex between the TP and 5'-dAMP. Increased 3'-5' exonucleolysis. 2 Publications1
Mutagenesisi457T → P: Complete loss of initiation and polymerization activities. Severe loss of protein-priming activity. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi458D → G: Complete loss of initiation and polymerization activities. Severe loss of protein-priming activity. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi498K → R: Strong decrease in DNA polymerization activity. Loss of binding to a primer-template DNA. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi498K → T: Strong decrease in initiation and DNA polymerization activities. Loss of binding to a primer-template DNA. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi500Y → S: Strong decrease in DNA polymerization activity and interaction with primer-template DNA. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi529K → A: Increased exonuclease activity and loss of primer elongation. Deficient in nucleotide incorporation. 1 Publication1
Mutagenesisi529K → E: Increased exonuclease activity and complete loss of primer elongation. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000465421 – 575DNA polymeraseAdd BLAST575

Proteomic databases

PRoteomics IDEntifications database

More...PRIDEi		P03680

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Keywords - Developmental stagei

Early protein

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Interacts with the primer terminal protein; this interaction allows the initiation of TP-primed DNA replication at both viral DNA ends.

Interacts with DNA.

3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei59Interaction with the primer terminal protein1 Publication1
Sitei61Interaction with the primer terminal protein1 Publication1
Sitei69Interaction with the primer terminal protein1 Publication1

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1575
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P03680

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P03680

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 1913'-5' exonuclease and strand displacement activities1 PublicationAdd BLAST191
Regioni192 – 229Involved in DNA-binding, coordination between DNA synthesis and degradation and TP interaction3 PublicationsAdd BLAST38
Regioni230 – 562Initiation, polymerization and pyrophosphorolytic activities1 PublicationAdd BLAST333
Regioni398 – 420TPR21 PublicationAdd BLAST23
Regioni563 – 575Involved in DNA-binding and TP interaction1 PublicationAdd BLAST13

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a short (usually not more than 20 amino acids) conserved sequence motif of biological significance.<p><a href='/help/motif' target='_top'>More...</a></p>Motifi454 – 458YCDTD1 Publication5

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The N-terminus contains the 3'-5' exonuclease activity and strand displacement ability (PubMed:8621470). The conserved motif YxGG/A located between the 3'-5' exonuclease and polymerization domains is important for DNA-binding, coordination between DNA synthesis and degradation and for the formation of a stable complex between TP and the DNA polymerase (PubMed:8670845, PubMed:9931249, PubMed:15777661). The C-terminus is involved in the protein-primed initiation, DNA polymerization and pyrophosphorolytic activities (PubMed:8621470, PubMed:1850426). The YCDTD motif is essential for the pyrophosphorolytic activity (PubMed:1850426). The TPR2 region is necessary for the strand displacement coupled to DNA synthesis and probably also for allowing the TP priming domain to move out from the polymerase during transition from initiation to elongation (PubMed:15845765, PubMed:19033368).6 Publications

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the DNA polymerase type-B family.Curated

Phylogenomic databases

KEGG Orthology (KO)

More...KOi		K21237

Database of Orthologous Groups

More...OrthoDBi		3801at10239

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.30.420.10, 1 hit
3.90.1600.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR006172 DNA-dir_DNA_pol_B
IPR017964 DNA-dir_DNA_pol_B_CS
IPR004868 DNA-dir_DNA_pol_B_mt/vir
IPR014416 DNA-dir_DNA_polB_phi29_vir
IPR023211 DNA_pol_palm_dom_sf
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf

Pfam protein domain database

More...Pfami		View protein in Pfam
PF03175 DNA_pol_B_2, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF004178 Dpol_Bac_phage, 1 hit

Protein Motif fingerprint database; a protein domain database

More...PRINTSi		PR00106 DNAPOLB

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00486 POLBc, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF53098 SSF53098, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS00116 DNA_POLYMERASE_B, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P03680-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKHMPRKMYS CDFETTTKVE DCRVWAYGYM NIEDHSEYKI GNSLDEFMAW 
        60         70         80         90        100
VLKVQADLYF HNLKFDGAFI INWLERNGFK WSADGLPNTY NTIISRMGQW 
       110        120        130        140        150
YMIDICLGYK GKRKIHTVIY DSLKKLPFPV KKIAKDFKLT VLKGDIDYHK 
       160        170        180        190        200
ERPVGYKITP EEYAYIKNDI QIIAEALLIQ FKQGLDRMTA GSDSLKGFKD 
       210        220        230        240        250
IITTKKFKKV FPTLSLGLDK EVRYAYRGGF TWLNDRFKEK EIGEGMVFDV 
       260        270        280        290        300
NSLYPAQMYS RLLPYGEPIV FEGKYVWDED YPLHIQHIRC EFELKEGYIP 
       310        320        330        340        350
TIQIKRSRFY KGNEYLKSSG GEIADLWLSN VDLELMKEHY DLYNVEYISG 
       360        370        380        390        400
LKFKATTGLF KDFIDKWTYI KTTSEGAIKQ LAKLMLNSLY GKFASNPDVT 
       410        420        430        440        450
GKVPYLKENG ALGFRLGEEE TKDPVYTPMG VFITAWARYT TITAAQACYD 
       460        470        480        490        500
RIIYCDTDSI HLTGTEIPDV IKDIVDPKKL GYWAHESTFK RAKYLRQKTY 
       510        520        530        540        550
IQDIYMKEVD GKLVEGSPDD YTDIKFSVKC AGMTDKIKKE VTFENFKVGF 
       560        570 
SRKMKPKPVQ VPGGVVLVDD TFTIK
Length:575
Mass (Da):66,714
Last modified:July 21, 1986 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i856EEB6B04A7E268
GO

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence ACE96023 differs from that shown. Reason: Erroneous initiation. Truncated N-terminus.

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti492A → V in CAA37450 (PubMed:2118623).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section describes natural variant(s) of the protein sequence.<p><a href='/help/variant' target='_top'>More...</a></p>Natural varianti176A → R in mutant TS2(24). 1
Natural varianti355A → V in mutant TS2(24). 1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
V01155 Genomic DNA Translation: CAA24480.1
X53370 Genomic DNA Translation: CAA37450.1
EU771092 Genomic DNA Translation: ACE96023.1 Different initiation.
X53371 Genomic DNA Translation: CAA37451.1

Protein sequence database of the Protein Information Resource

More...PIRi		A04282 ERBP29

NCBI Reference Sequences

More...RefSeqi		YP_002004529.1, NC_011048.1

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...GeneIDi		6446511

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		vg:6446511

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01155 Genomic DNA Translation: CAA24480.1
X53370 Genomic DNA Translation: CAA37450.1
EU771092 Genomic DNA Translation: ACE96023.1 Different initiation.
X53371 Genomic DNA Translation: CAA37451.1
PIRiA04282 ERBP29
RefSeqiYP_002004529.1, NC_011048.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1XHXX-ray2.35A/B/C/D1-575[»]
1XHZX-ray2.70A/B/C/D1-575[»]
1XI1X-ray2.20A/B1-575[»]
2EX3X-ray3.00A/C/E/G/I/K1-575[»]
2PY5X-ray1.60A/B1-575[»]
2PYJX-ray2.03A/B1-575[»]
2PYLX-ray2.20A1-575[»]
2PZSX-ray2.60A/B/C/D1-575[»]
SMRiP03680
ModBaseiSearch...
PDBe-KBiSearch...

Proteomic databases

PRIDEiP03680

Genome annotation databases

GeneIDi6446511
KEGGivg:6446511

Phylogenomic databases

KOiK21237
OrthoDBi3801at10239

Miscellaneous databases

EvolutionaryTraceiP03680

Family and domain databases

Gene3Di3.30.420.10, 1 hit
3.90.1600.10, 1 hit
InterProiView protein in InterPro
IPR006172 DNA-dir_DNA_pol_B
IPR017964 DNA-dir_DNA_pol_B_CS
IPR004868 DNA-dir_DNA_pol_B_mt/vir
IPR014416 DNA-dir_DNA_polB_phi29_vir
IPR023211 DNA_pol_palm_dom_sf
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf
PfamiView protein in Pfam
PF03175 DNA_pol_B_2, 1 hit
PIRSFiPIRSF004178 Dpol_Bac_phage, 1 hit
PRINTSiPR00106 DNAPOLB
SMARTiView protein in SMART
SM00486 POLBc, 1 hit
SUPFAMiSSF53098 SSF53098, 1 hit
PROSITEiView protein in PROSITE
PS00116 DNA_POLYMERASE_B, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiDPOL_BPPH2
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P03680
Secondary accession number(s): B3VMN6, Q38545
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: October 16, 2019
This is version 127 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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