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UniProtKB - Q9V2F3 (DP2S_PYRAB)

Entry version 123 (25 May 2022)
Sequence version 1 (01 May 2000)
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Protein

DNA polymerase II small subunit

Gene

polB

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
Status
Reviewed-Annotation 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>-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

Possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3' to 5' direction. Has a template-primer preference which is characteristic of a replicative DNA polymerase (By similarity).

By similarity

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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

  • Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates. EC:3.1.11.1

<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, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, Transferase
Biological processDNA replication

Enzyme and pathway databases

BRENDA Comprehensive Enzyme Information System

More...BRENDAi		2.7.7.7, 5242

<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%5Fand%5Ftaxonomy%5Fsection">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 II small subunit (EC:2.7.7.7)
Short name:
Pol II
Alternative name(s):
Exodeoxyribonuclease small subunit (EC:3.1.11.1)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
Ordered Locus Names:PYRAB01210
ORF Names:PAB2266
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiPyrococcus abyssi (strain GE5 / Orsay)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri272844 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiArchaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000000810 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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: Chromosome
  • UP000009139 Componenti: Chromosome

<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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000961791 – 619DNA polymerase II small subunitAdd BLAST619

<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%5Fsection">'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%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Heterodimer of a large subunit and a small subunit.

By similarity

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		272844.PAB2266

<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

1619
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

AlphaFold Protein Structure Database

More...AlphaFoldDBi		Q9V2F3

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

More...SMRi		Q9V2F3

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		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>Regioni78 – 122DisorderedSequence analysisAdd BLAST45

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular type of amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi78 – 92Basic and acidic residuesSequence analysisAdd BLAST15
Compositional biasi93 – 108Polar residuesSequence analysisAdd BLAST16

<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 delta/II small subunit family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		arCOG04455, Archaea

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_027850_1_0_2

Identification of Orthologs from Complete Genome Data

More...OMAi		FIGPGNH

Database of Orthologous Groups

More...OrthoDBi		11652at2157

Database for complete collections of gene phylogenies

More...PhylomeDBi		Q9V2F3

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		2.40.50.140, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_00325, DNApol_II_A_arch, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR007185, DNA_pol_a/d/e_bsu
IPR024826, DNA_pol_delta/II_ssu
IPR029052, Metallo-depent_PP-like
IPR012340, NA-bd_OB-fold
IPR011149, Pol2_small_arc

The PANTHER Classification System

More...PANTHERi		PTHR10416, PTHR10416, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF04042, DNA_pol_E_B, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF000803, Arc_Pol2_small, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF50249, SSF50249, 1 hit
SSF56300, SSF56300, 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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

Q9V2F3-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDELVKALER AGYLLTPSAY YLLVDHFKEG KFSLVELVKF AKSKGVFIID 
        60         70         80         90        100
GDLAYEFLQF LGLGVPQEIK ESYISTGEEA EKTVESQETR ASELEEGGVS 
       110        120        130        140        150
QVSSGELQEL KEESPEISTT EEEIGGLELV QSSISTGSEV EYNNGENGES 
       160        170        180        190        200
VVVLDKYGYP ILYAPEEIGE EKEYSKYEDV VIEWNPSVTP VQIEKNYEVK 
       210        220        230        240        250
FDVRQVKLRP PKVKNGSGKE GEIIVEAYAS LFKSRLSKLK RILRENPEIS 
       260        270        280        290        300
NVVDIGKLNY VSGDEEVTII GLVNSKRETN RGLIFEVEDK TGIVKVFLPK 
       310        320        330        340        350
DSEDYREAFK VLPDAVVAFK GFYSKKGIFF ANKFYLPDVP LYRKQKPPLE 
       360        370        380        390        400
EKVYAILISD IHVGSREFCE KAFLKFLEWL NGHVESKEEE EIVSRVKYLI 
       410        420        430        440        450
IAGDVVDGIG IYPGQYSDLV IPDIFDQYEA LANLLANVPE HITMFIGPGN 
       460        470        480        490        500
HDAARPAIPQ PEFYKEYAKP IYKLKNAIII SNPAVIRLHG RDFLIAHGRG 
       510        520        530        540        550
IEDVVSFVPG LTHHKPGLPM VELLKMRHLA PTFGGKVPIA PDPEDLLVIE 
       560        570        580        590        600
EVPDLVQMGH VHVYDAVVYR GVQLVNSATW QAQTEFQKMV NIVPTPAKVP 
       610 
VVDVESARVV KVLDFSGWC
Length:619
Mass (Da):69,395
Last modified:May 1, 2000 - 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:iF556800288784814
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
AJ248283 Genomic DNA Translation: CAB49045.1
HE613800 Genomic DNA Translation: CCE69497.1

Protein sequence database of the Protein Information Resource

More...PIRi		F75199

NCBI Reference Sequences

More...RefSeqi		WP_010867245.1, NC_000868.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		CAB49045; CAB49045; PAB2266

Database of genes from NCBI RefSeq genomes

More...GeneIDi		1495008

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		pab:PAB2266

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|272844.11.peg.134

<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
AJ248283 Genomic DNA Translation: CAB49045.1
HE613800 Genomic DNA Translation: CCE69497.1
PIRiF75199
RefSeqiWP_010867245.1, NC_000868.1

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
5IHEX-ray2.50A/B145-619[»]
6HMFX-ray2.60A/B145-619[»]
6HMSelectron microscopy7.10A225-619[»]
6T8Helectron microscopy3.77A1-619[»]
AlphaFoldDBiQ9V2F3
SMRiQ9V2F3
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi272844.PAB2266

Genome annotation databases

EnsemblBacteriaiCAB49045; CAB49045; PAB2266
GeneIDi1495008
KEGGipab:PAB2266
PATRICifig|272844.11.peg.134

Phylogenomic databases

eggNOGiarCOG04455, Archaea
HOGENOMiCLU_027850_1_0_2
OMAiFIGPGNH
OrthoDBi11652at2157
PhylomeDBiQ9V2F3

Enzyme and pathway databases

BRENDAi2.7.7.7, 5242

Family and domain databases

Gene3Di2.40.50.140, 1 hit
HAMAPiMF_00325, DNApol_II_A_arch, 1 hit
InterProiView protein in InterPro
IPR007185, DNA_pol_a/d/e_bsu
IPR024826, DNA_pol_delta/II_ssu
IPR029052, Metallo-depent_PP-like
IPR012340, NA-bd_OB-fold
IPR011149, Pol2_small_arc
PANTHERiPTHR10416, PTHR10416, 1 hit
PfamiView protein in Pfam
PF04042, DNA_pol_E_B, 1 hit
PIRSFiPIRSF000803, Arc_Pol2_small, 1 hit
SUPFAMiSSF50249, SSF50249, 1 hit
SSF56300, SSF56300, 1 hit

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 nameiDP2S_PYRAB
<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: Q9V2F3
Secondary accession number(s): G8ZFV6
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: May 1, 2000
Last modified: May 25, 2022
This is version 123 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 programProkaryotic 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

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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