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UniProtKB - Q51334 (DPOL_PYRSD)

Entry version 132 (25 May 2022)
Sequence version 1 (01 Nov 1996)
Previous versions | rss
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Protein

DNA polymerase

Gene

pol

Organism
Pyrococcus sp. (strain GB-D)
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

In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.

By similarity

Intein encoded endonucleases are thought to mediate intein mobility by site-specific recombination initiated by endonuclease cleavage at the 'homing site' in gene that lack the intein (Probable). Intein splicing has been shown to occur via a branched intermediate that is resolved as the reaction proceeds; formation of the branched intermediate is reversible in response to pH shifts (PubMed:8269515).

Curated1 Publication

<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

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>pH dependencei

Optimum pH for intein splicing is 4.5-6.5.1 Publication

<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, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase
Biological processDNA replication, Intron homing

Protein family/group databases

Restriction enzymes and methylases database

More...REBASEi		2619, PI-PspI

<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 (EC:2.7.7.7)
Alternative name(s):
Deep vent DNA polymerase
Cleaved into the following chain:
Homing endonuclease PI-PspI2 Publications (EC:3.1.-.-1 Publication)
Alternative name(s):
Psp-GDB pol intein
<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:pol
<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 sp. (strain GB-D)
<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 identifieri69013 [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 › unclassified Pyrococcus

<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

<p>This subsection of the 'Pathology and Biotech' section describes the use of a specific protein in the biotechnological industry.<p><a href='/help/biotechnological_use' target='_top'>More...</a></p>Biotechnological usei

Used in the PCR method because of its high thermostability and low error rate. Sold by New England Biolabs.

<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_00000073301 – 492DNA polymerase, 1st partAdd BLAST492
ChainiPRO_0000007331493 – 1029Homing endonuclease PI-PspI1 PublicationAdd BLAST537
ChainiPRO_00000073321030 – 1312DNA polymerase, 2nd partAdd BLAST283

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

This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation.1 Publication

Keywords - PTMi

Autocatalytic cleavage, Protein splicing

<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

11312
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

AlphaFold Protein Structure Database

More...AlphaFoldDBi		Q51334

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

More...SMRi		Q51334

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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini773 – 906DOD-type homing endonucleasePROSITE-ProRule annotationAdd BLAST134

<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

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		1.10.132.60, 1 hit
3.10.28.10, 1 hit
3.30.420.10, 1 hit
3.90.1600.10, 2 hits

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
IPR006133, DNA-dir_DNA_pol_B_exonuc
IPR006134, DNA-dir_DNA_pol_B_multi_dom
IPR043502, DNA/RNA_pol_sf
IPR042087, DNA_pol_B_thumb
IPR023211, DNA_pol_palm_dom_sf
IPR021133, HEAT_type_2
IPR003586, Hint_dom_C
IPR003587, Hint_dom_N
IPR036844, Hint_dom_sf
IPR027434, Homing_endonucl
IPR006142, INTEIN
IPR030934, Intein_C
IPR004042, Intein_endonuc
IPR006141, Intein_N
IPR004860, LAGLIDADG_2
IPR041005, PI-TkoII_IV
IPR012337, RNaseH-like_sf
IPR036397, RNaseH_sf

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00136, DNA_pol_B, 2 hits
PF03104, DNA_pol_B_exo1, 2 hits
PF14528, LAGLIDADG_3, 1 hit
PF18714, PI-TkoII_IV, 1 hit

Protein Motif fingerprint database; a protein domain database

More...PRINTSi		PR00106, DNAPOLB
PR00379, INTEIN

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00305, HintC, 1 hit
SM00306, HintN, 1 hit
SM00486, POLBc, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF51294, SSF51294, 1 hit
SSF53098, SSF53098, 1 hit
SSF55608, SSF55608, 1 hit
SSF56672, SSF56672, 2 hits

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR01443, intein_Cterm, 1 hit
TIGR01445, intein_Nterm, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS00116, DNA_POLYMERASE_B, 1 hit
PS50818, INTEIN_C_TER, 1 hit
PS50819, INTEIN_ENDONUCLEASE, 1 hit
PS50817, INTEIN_N_TER, 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.

<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 in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

Q51334-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MILDADYITE DGKPIIRIFK KENGEFKVEY DRNFRPYIYA LLKDDSQIDE 
        60         70         80         90        100
VRKITAERHG KIVRIIDAEK VRKKFLGRPI EVWRLYFEHP QDVPAIRDKI 
       110        120        130        140        150
REHSAVIDIF EYDIPFAKRY LIDKGLIPME GDEELKLLAF DIETLYHEGE 
       160        170        180        190        200
EFAKGPIIMI SYADEEEAKV ITWKKIDLPY VEVVSSEREM IKRFLKVIRE 
       210        220        230        240        250
KDPDVIITYN GDSFDLPYLV KRAEKLGIKL PLGRDGSEPK MQRLGDMTAV 
       260        270        280        290        300
EIKGRIHFDL YHVIRRTINL PTYTLEAVYE AIFGKPKEKV YAHEIAEAWE 
       310        320        330        340        350
TGKGLERVAK YSMEDAKVTY ELGREFFPME AQLSRLVGQP LWDVSRSSTG 
       360        370        380        390        400
NLVEWYLLRK AYERNELAPN KPDEREYERR LRESYAGGYV KEPEKGLWEG 
       410        420        430        440        450
LVSLDFRSLY PSIIITHNVS PDTLNREGCR EYDVAPEVGH KFCKDFPGFI 
       460        470        480        490        500
PSLLKRLLDE RQEIKRKMKA SKDPIEKKML DYRQRAIKIL ANSILPEEWV 
       510        520        530        540        550
PLIKNGKVKI FRIGDFVDGL MKANQGKVKK TGDTEVLEVA GIHAFSFDRK 
       560        570        580        590        600
SKKARVMAVK AVIRHRYSGN VYRIVLNSGR KITITEGHSL FVYRNGDLVE 
       610        620        630        640        650
ATGEDVKIGD LLAVPRSVNL PEKRERLNIV ELLLNLSPEE TEDIILTIPV 
       660        670        680        690        700
KGRKNFFKGM LRTLRWIFGE EKRVRTASRY LRHLENLGYI RLRKIGYDII 
       710        720        730        740        750
DKEGLEKYRT LYEKLVDVVR YNGNKREYLV EFNAVRDVIS LMPEEELKEW 
       760        770        780        790        800
RIGTRNGFRM GTFVDIDEDF AKLLGYYVSE GSARKWKNQT GGWSYTVRLY 
       810        820        830        840        850
NENDEVLDDM EHLAKKFFGK VKRGKNYVEI PKKMAYIIFE SLCGTLAENK 
       860        870        880        890        900
RVPEVIFTSS KGVRWAFLEG YFIGDGDVHP SKRVRLSTKS ELLVNGLVLL 
       910        920        930        940        950
LNSLGVSAIK LGYDSGVYRV YVNEELKFTE YRKKKNVYHS HIVPKDILKE 
       960        970        980        990       1000
TFGKVFQKNI SYKKFRELVE NGKLDREKAK RIEWLLNGDI VLDRVVEIKR 
      1010       1020       1030       1040       1050
EYYDGYVYDL SVDEDENFLA GFGFLYAHNS YYGYYGYAKA RWYCKECAES 
      1060       1070       1080       1090       1100
VTAWGREYIE FVRKELEEKF GFKVLYIDTD GLYATIPGAK PEEIKKKALE 
      1110       1120       1130       1140       1150
FVDYINAKLP GLLELEYEGF YVRGFFVTKK KYALIDEEGK IITRGLEIVR 
      1160       1170       1180       1190       1200
RDWSEIAKET QAKVLEAILK HGNVEEAVKI VKEVTEKLSK YEIPPEKLVI 
      1210       1220       1230       1240       1250
YEQITRPLHE YKAIGPHVAV AKRLAARGVK VRPGMVIGYI VLRGDGPISK 
      1260       1270       1280       1290       1300
RAILAEEFDL RKHKYDAEYY IENQVLPAVL RILEAFGYRK EDLRWQKTKQ 
      1310 
TGLTAWLNIK KK
Length:1,312
Mass (Da):152,854
Last modified:November 1, 1996 - 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:iB62518805641D26A
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
U00707 Genomic DNA Translation: AAA67130.1
U00707 Genomic DNA Translation: AAA67131.1
U00707 Genomic DNA Translation: AAA67132.1

Protein sequence database of the Protein Information Resource

More...PIRi		S68593

<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
U00707 Genomic DNA Translation: AAA67130.1
U00707 Genomic DNA Translation: AAA67131.1
U00707 Genomic DNA Translation: AAA67132.1
PIRiS68593

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
5H12X-ray2.50A1-1312[»]
AlphaFoldDBiQ51334
SMRiQ51334
ModBaseiSearch...
PDBe-KBiSearch...

Protein family/group databases

REBASEi2619, PI-PspI

Family and domain databases

Gene3Di1.10.132.60, 1 hit
3.10.28.10, 1 hit
3.30.420.10, 1 hit
3.90.1600.10, 2 hits
InterProiView protein in InterPro
IPR006172, DNA-dir_DNA_pol_B
IPR017964, DNA-dir_DNA_pol_B_CS
IPR006133, DNA-dir_DNA_pol_B_exonuc
IPR006134, DNA-dir_DNA_pol_B_multi_dom
IPR043502, DNA/RNA_pol_sf
IPR042087, DNA_pol_B_thumb
IPR023211, DNA_pol_palm_dom_sf
IPR021133, HEAT_type_2
IPR003586, Hint_dom_C
IPR003587, Hint_dom_N
IPR036844, Hint_dom_sf
IPR027434, Homing_endonucl
IPR006142, INTEIN
IPR030934, Intein_C
IPR004042, Intein_endonuc
IPR006141, Intein_N
IPR004860, LAGLIDADG_2
IPR041005, PI-TkoII_IV
IPR012337, RNaseH-like_sf
IPR036397, RNaseH_sf
PfamiView protein in Pfam
PF00136, DNA_pol_B, 2 hits
PF03104, DNA_pol_B_exo1, 2 hits
PF14528, LAGLIDADG_3, 1 hit
PF18714, PI-TkoII_IV, 1 hit
PRINTSiPR00106, DNAPOLB
PR00379, INTEIN
SMARTiView protein in SMART
SM00305, HintC, 1 hit
SM00306, HintN, 1 hit
SM00486, POLBc, 1 hit
SUPFAMiSSF51294, SSF51294, 1 hit
SSF53098, SSF53098, 1 hit
SSF55608, SSF55608, 1 hit
SSF56672, SSF56672, 2 hits
TIGRFAMsiTIGR01443, intein_Cterm, 1 hit
TIGR01445, intein_Nterm, 1 hit
PROSITEiView protein in PROSITE
PS00116, DNA_POLYMERASE_B, 1 hit
PS50818, INTEIN_C_TER, 1 hit
PS50819, INTEIN_ENDONUCLEASE, 1 hit
PS50817, INTEIN_N_TER, 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 nameiDPOL_PYRSD
<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: Q51334
Secondary accession number(s): Q51335, Q51336
<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: November 1, 1997
Last sequence update: November 1, 1996
Last modified: May 25, 2022
This is version 132 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, Direct protein sequencing

Documents

  1. Intein-containing proteins
    List of intein-containing protein entries
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
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