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Entry version 103 (16 Oct 2019)
Sequence version 2 (13 Sep 2005)
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Protein

DNA polymerase beta

Gene

polb

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
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 transcript 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

Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases (By similarity).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 similarityNote: Binds 2 magnesium ions per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei71Schiff-base intermediate with DNABy similarity1
<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 bindingi100Sodium; via carbonyl oxygenBy similarity1
Metal bindingi102Sodium; via carbonyl oxygenBy similarity1
Metal bindingi105Sodium; via carbonyl oxygenBy similarity1
Metal bindingi189Magnesium 1By similarity1
Metal bindingi189Magnesium 2By similarity1
Metal bindingi191Magnesium 1By similarity1
Metal bindingi191Magnesium 2By similarity1
Metal bindingi257Magnesium 2By 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, Lyase, Nucleotidyltransferase, Transferase
Biological processDNA damage, DNA repair, DNA replication, DNA synthesis
LigandMagnesium, Metal-binding, Sodium

Enzyme and pathway databases

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
2.7.7.7 928

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-DRE-110362 POLB-Dependent Long Patch Base Excision Repair
R-DRE-110373 Resolution of AP sites via the multiple-nucleotide patch replacement pathway
R-DRE-110381 Resolution of AP sites via the single-nucleotide replacement pathway
R-DRE-5649702 APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway
R-DRE-5651801 PCNA-Dependent Long Patch Base Excision Repair
R-DRE-5689880 Ub-specific processing proteases
R-DRE-73930 Abasic sugar-phosphate removal via the single-nucleotide replacement pathway

<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 beta (EC:2.7.7.7, EC:4.2.99.-)
<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:polb
<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>OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
<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 identifieri7955 [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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
<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
  • UP000000437 <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: Unplaced

Organism-specific databases

Zebrafish Information Network genome database

More...
ZFINi
ZDB-GENE-040830-1 polb

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

<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_00002187811 – 336DNA polymerase betaAdd BLAST336

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei82Omega-N-methylarginine; by PRMT6By similarity1
Modified residuei151Omega-N-methylarginine; by PRMT6By similarity1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Methylation by PRMT6 stimulates the polymerase activity by enhancing DNA binding and processivity.By similarity
Ubiquitinated: monoubiquitinated by huwe1/arf-bp1. Monoubiquitinated protein is then the target of stub1/chip, which catalyzes polyubiquitination from monoubiquitin, leading to degradation by the proteasome. usp47 mediates the deubiquitination of monoubiquitinated protein, preventing polyubiquitination by STUB1/CHIP and its subsequent degradation (By similarity).By similarity

Keywords - PTMi

Methylation, Ubl conjugation

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
Q6DRD3

PeptideAtlas

More...
PeptideAtlasi
Q6DRD3

<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

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
7955.ENSDARP00000017489

<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
Q6DRD3

Database of comparative protein structure models

More...
ModBasei
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>Regioni182 – 191DNA bindingBy similarity10

<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-X family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG2534 Eukaryota
COG1796 LUCA

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q6DRD3

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00141 NT_POLXc, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.150.110, 1 hit
3.30.210.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR002054 DNA-dir_DNA_pol_X
IPR019843 DNA_pol-X_BS
IPR010996 DNA_pol_b-like_N
IPR028207 DNA_pol_B_palm_palm
IPR018944 DNA_pol_lambd_fingers_domain
IPR027421 DNA_pol_lamdba_lyase_dom_sf
IPR037160 DNA_Pol_thumb_sf
IPR022312 DNA_pol_X
IPR002008 DNA_pol_X_beta-like
IPR003583 Hlx-hairpin-Hlx_DNA-bd_motif
IPR029398 PolB_thumb

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF14792 DNA_pol_B_palm, 1 hit
PF14791 DNA_pol_B_thumb, 1 hit
PF10391 DNA_pol_lambd_f, 1 hit
PF14716 HHH_8, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR00869 DNAPOLX
PR00870 DNAPOLXBETA

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00278 HhH1, 2 hits
SM00483 POLXc, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF47802 SSF47802, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00522 DNA_POLYMERASE_X, 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>Sequence (1+)i

<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.

This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.Show allAlign All

Q6DRD3-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
SKRKAPQESL NEGITDFLVE LANYERNVNR AIHKYNAYRK AASVIAKYPQ
60 70 80 90 100
KIKSGTEAKK LDGVGAKIAE KIDEFLTTGK LRKLEKIRND DTSSSINFLT
110 120 130 140 150
RVTGIGPAAA RKFFDEGVRN LEDLKKIEHK LNHHQQIGLK YFEEFEKRIP
160 170 180 190 200
RSEMQKMEAL ILKELDIVDP EYIGTICGSY RRGAESSGDI DILLTHPDFT
210 220 230 240 250
SQSEKQPKLL HAVVDHLESI GFITDTLSKG DTKFMGVCQL QKEKEEEEEE
260 270 280 290 300
SLHRRIDIRL IPKDQYYCGV LYFTGSDIFN KNMRTHALEK GFTLNEYTIR
310 320 330
PLGVTGVAGE PLLVDSEKDI FEYIQWKYRE PKDRSE
Length:336
Mass (Da):38,566
Last modified:September 13, 2005 - v2
<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:iFDF6EA3088354973
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
B0R195B0R195_DANRE
DNA polymerase
polb
291Annotation score:

Annotation score:3 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>
B0R194B0R194_DANRE
DNA polymerase
polb
339Annotation score:

Annotation score:2 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>

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
AY648826 mRNA Translation: AAT68144.1

<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
AY648826 mRNA Translation: AAT68144.1

3D structure databases

SMRiQ6DRD3
ModBaseiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000017489

Proteomic databases

PaxDbiQ6DRD3
PeptideAtlasiQ6DRD3

Organism-specific databases

ZFINiZDB-GENE-040830-1 polb

Phylogenomic databases

eggNOGiKOG2534 Eukaryota
COG1796 LUCA
InParanoidiQ6DRD3

Enzyme and pathway databases

BRENDAi2.7.7.7 928
ReactomeiR-DRE-110362 POLB-Dependent Long Patch Base Excision Repair
R-DRE-110373 Resolution of AP sites via the multiple-nucleotide patch replacement pathway
R-DRE-110381 Resolution of AP sites via the single-nucleotide replacement pathway
R-DRE-5649702 APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway
R-DRE-5651801 PCNA-Dependent Long Patch Base Excision Repair
R-DRE-5689880 Ub-specific processing proteases
R-DRE-73930 Abasic sugar-phosphate removal via the single-nucleotide replacement pathway

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q6DRD3

Family and domain databases

CDDicd00141 NT_POLXc, 1 hit
Gene3Di1.10.150.110, 1 hit
3.30.210.10, 1 hit
InterProiView protein in InterPro
IPR002054 DNA-dir_DNA_pol_X
IPR019843 DNA_pol-X_BS
IPR010996 DNA_pol_b-like_N
IPR028207 DNA_pol_B_palm_palm
IPR018944 DNA_pol_lambd_fingers_domain
IPR027421 DNA_pol_lamdba_lyase_dom_sf
IPR037160 DNA_Pol_thumb_sf
IPR022312 DNA_pol_X
IPR002008 DNA_pol_X_beta-like
IPR003583 Hlx-hairpin-Hlx_DNA-bd_motif
IPR029398 PolB_thumb
PfamiView protein in Pfam
PF14792 DNA_pol_B_palm, 1 hit
PF14791 DNA_pol_B_thumb, 1 hit
PF10391 DNA_pol_lambd_f, 1 hit
PF14716 HHH_8, 1 hit
PRINTSiPR00869 DNAPOLX
PR00870 DNAPOLXBETA
SMARTiView protein in SMART
SM00278 HhH1, 2 hits
SM00483 POLXc, 1 hit
SUPFAMiSSF47802 SSF47802, 1 hit
PROSITEiView protein in PROSITE
PS00522 DNA_POLYMERASE_X, 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 nameiDPOLB_DANRE
<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: Q6DRD3
<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: September 13, 2005
Last sequence update: September 13, 2005
Last modified: October 16, 2019
This is version 103 of the entry and version 2 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 programChordata 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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