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Protein

DNA polymerase

Gene

2

Organism
Bacillus phage Nf (Bacteriophage Nf)
Status
Reviewed-Annotation score:

Annotation score:4 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 (By similarity). 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:23110220). 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 third T at the 3' end, and 3' to 5' exonuclease activity (PubMed:23110220, PubMed:19011105). Exonuclease activity has a proofreading purpose (By similarity). Since the polymerase initiates the replication on the third thymine, the TP-dAMP initiation product translocates backwards to recover the template information of the 2 terminal nucleotide (sliding back-mechanism) (PubMed:23110220, PubMed:19011105).By similarity2 Publications

Miscellaneous

This DNA polymerase requires a protein as a primer.By similarity

<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+By similarity

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>Sitei9Essential for 3'-5' exonucleolysisBy similarity1
Sitei11Essential for 3'-5' exonucleolysisBy similarity1
Sitei62Essential for 3'-5' exonucleolysisBy similarity1
Sitei90Involved in binding template-primer structuresBy similarity1
Sitei119Essential for 3'-5' exonucleolysisBy similarity1
Sitei120Essential for 3'-5' exonucleolysisBy similarity1
<p>This subsection of the ‘Function’ 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 bindingi142Magnesium 1By similarity1
Metal bindingi166Magnesium 1By similarity1
Metal bindingi246Magnesium 2; catalyticBy similarity1
Metal bindingi247Magnesium 2; via carbonyl oxygenBy similarity1
Sitei249Probably involved in binding template-primer structuresBy similarity1
<p>This subsection of the ‘Function’ 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 sitei251TTP; via amide nitrogenBy similarity1
Sitei251Probably involved in nucleotide binding selectionBy similarity1
Binding sitei368TTPBy similarity1
Binding sitei380TTPBy similarity1
Sitei380Probably involved in nucleotide binding selectionBy similarity1
Sitei384Probably involved in binding template-primer structuresBy similarity1
Sitei387Probably involved in nucleotide binding selectionBy similarity1
Sitei388Probably involved in binding template-primer structuresBy similarity1
Sitei431Probably involved in binding template-primer structuresBy similarity1
Sitei435Probably involved in binding template-primer structuresBy similarity1
Metal bindingi453Magnesium 2; catalyticBy similarity1
Metal bindingi455Magnesium 2; catalyticBy similarity1
Binding sitei455TTPBy similarity1
Sitei495Probably involved in binding template-primer structuresBy similarity1
Sitei497Probably involved in binding template-primer structuresBy similarity1
Sitei526Stabilizes the primer-terminus at the polymerization active site and contributes to the coordination between the exonuclease and polymerazation activitiesBy similarity1

<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

GO - Biological processi

<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.-By similarity)
Alternative name(s):
Gene product 2Curated
Short name:
gp2Curated
Protein p2
<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:2Imported
<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 Nf (Bacteriophage Nf)
<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 identifieri10753 [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 lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesPodoviridaePicovirinaePhi29virus
<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
  • UP000000744 <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 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_00004360721 – 572DNA polymeraseAdd BLAST572

<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.By similarity

<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

3D structure databases

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

More...
SMRi
B7SSM2

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<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 – 2223'-5' exonuclease and strand displacement activitiesBy similarityAdd BLAST222
Regioni56 – 66Interaction with the primer terminal proteinBy similarityAdd BLAST11
Regioni223 – 226DNA-binding; Involved in the formation of a stable complex between TP and phi29 DNA polymeraseBy similarity4
Regioni227 – 572Initiation, polymerization and pyrophosphorolytic activitiesBy similarityAdd BLAST346

<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. The C-terminus contains the protein-primed initiation, DNA polymerization and pyrophosphorolytic activities.By similarity

<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

Database of Orthologous Groups

More...
OrthoDBi
VOG0900004K

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>.<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.

B7SSM2-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSRKMFSCDF ETTTKLDDCR VWAYGYMEIG NLDNYKIGNS LDEFMQWVME
60 70 80 90 100
IQADLYFHNL KFDGAFIVNW LEQHGFKWSN EGLPNTYNTI ISKMGQWYMI
110 120 130 140 150
DICFGYRGKR KLHTVIYDSL KKLPFPVKKI AKDFQLPLLK GDIDYHTERP
160 170 180 190 200
VGHEITPEEY EYIKNDIEII ARALDIQFKQ GLDRMTAGSD SLKGFKDILS
210 220 230 240 250
TKKFNKVFPK LSLPMDKEIR KAYRGGFTWL NDKYKEKEIG EGMVFDVNSL
260 270 280 290 300
YPSQMYSRPL PYGAPIVFQG KYEKDEQYPL YIQRIRFEFE LKEGYIPTIQ
310 320 330 340 350
IKKNPFFKGN EYLKNSGVEP VELYLTNVDL ELIQEHYELY NVEYIDGFKF
360 370 380 390 400
REKTGLFKDF IDKWTYVKTH EEGAKKQLAK LMLNSLYGKF ASNPDVTGKV
410 420 430 440 450
PYLKDDGSLG FRVGDEEYKD PVYTPMGVFI TAWARFTTIT AAQACYDRII
460 470 480 490 500
YCDTDSIHLT GTEVPEIIKD IVDPKKLGYW AHESTFKRAK YLRQKTYIQD
510 520 530 540 550
IYVKEVDGKL KECSPDEATT TKFSVKCAGM TDTIKKKVTF DNFAVGFSSM
560 570
GKPKPVQVNG GVVLVDSVFT IK
Length:572
Mass (Da):66,451
Last modified:February 10, 2009 - 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:i8E260DFCFC981F76
GO

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
EU622808 Genomic DNA Translation: ACH57069.1

<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
EU622808 Genomic DNA Translation: ACH57069.1

3D structure databases

SMRiB7SSM2
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

OrthoDBiVOG0900004K

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...

<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_BPNF
<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: B7SSM2
<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: May 11, 2016
Last sequence update: February 10, 2009
Last modified: December 5, 2018
This is version 43 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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