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Q51334

- DPOL_PYRSD

UniProt

Q51334 - DPOL_PYRSD

Protein

DNA polymerase

Gene

pol

Organism
Pyrococcus sp. (strain GB-D)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 1 (01 Nov 1996)
      Previous versions | rss
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    Functioni

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

    Catalytic activityi

    Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. DNA-directed DNA polymerase activity Source: UniProtKB-KW
    3. endonuclease activity Source: UniProtKB-KW
    4. nucleotide binding Source: InterPro

    GO - Biological processi

    1. intein-mediated protein splicing Source: InterPro
    2. intron homing Source: UniProtKB-KW

    Keywords - Molecular functioni

    DNA-directed DNA polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    DNA replication, Intron homing

    Keywords - Ligandi

    DNA-binding

    Protein family/group databases

    REBASEi2619. PI-PspI.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA polymerase (EC:2.7.7.7)
    Alternative name(s):
    Deep vent DNA polymerase
    Cleaved into the following chain:
    Alternative name(s):
    Psp-GDB pol intein
    Gene namesi
    Name:pol
    OrganismiPyrococcus sp. (strain GB-D)
    Taxonomic identifieri69013 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus

    Pathology & Biotechi

    Biotechnological usei

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

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 492492DNA polymerase, 1st partPRO_0000007330Add
    BLAST
    Chaini493 – 1029537Endonuclease PI-PspIPRO_0000007331Add
    BLAST
    Chaini1030 – 1312283DNA polymerase, 2nd partPRO_0000007332Add
    BLAST

    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.

    Keywords - PTMi

    Autocatalytic cleavage, Protein splicing

    Structurei

    3D structure databases

    ProteinModelPortaliQ51334.
    SMRiQ51334. Positions 1-1310.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini773 – 906134DOD-type homing endonucleasePROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the DNA polymerase type-B family.Curated
    Contains 1 DOD-type homing endonuclease domain.PROSITE-ProRule annotation

    Family and domain databases

    Gene3Di2.170.16.10. 2 hits.
    3.10.28.10. 2 hits.
    3.30.420.10. 1 hit.
    3.90.1600.10. 2 hits.
    InterProiIPR006172. 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.
    IPR023211. DNA_pol_palm_dom.
    IPR021133. HEAT_type_2.
    IPR028992. Hedgehog/Intein_dom.
    IPR003586. Hint_dom_C.
    IPR003587. Hint_dom_N.
    IPR027434. Homing_endonucl.
    IPR006142. INTEIN.
    IPR004042. Intein_endonuc.
    IPR006141. Intein_splice_site.
    IPR012337. RNaseH-like_dom.
    [Graphical view]
    PfamiPF00136. DNA_pol_B. 2 hits.
    PF03104. DNA_pol_B_exo1. 2 hits.
    PF14528. LAGLIDADG_3. 1 hit.
    [Graphical view]
    PRINTSiPR00106. DNAPOLB.
    PR00379. INTEIN.
    SMARTiSM00305. HintC. 1 hit.
    SM00306. HintN. 1 hit.
    SM00486. POLBc. 1 hit.
    [Graphical view]
    SUPFAMiSSF51294. SSF51294. 2 hits.
    SSF53098. SSF53098. 1 hit.
    SSF55608. SSF55608. 1 hit.
    TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
    TIGR01445. intein_Nterm. 1 hit.
    PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
    PS50818. INTEIN_C_TER. 1 hit.
    PS50819. INTEIN_ENDONUCLEASE. 1 hit.
    PS50817. INTEIN_N_TER. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q51334-1 [UniParc]FASTAAdd to Basket

    « Hide

    MILDADYITE DGKPIIRIFK KENGEFKVEY DRNFRPYIYA LLKDDSQIDE     50
    VRKITAERHG KIVRIIDAEK VRKKFLGRPI EVWRLYFEHP QDVPAIRDKI 100
    REHSAVIDIF EYDIPFAKRY LIDKGLIPME GDEELKLLAF DIETLYHEGE 150
    EFAKGPIIMI SYADEEEAKV ITWKKIDLPY VEVVSSEREM IKRFLKVIRE 200
    KDPDVIITYN GDSFDLPYLV KRAEKLGIKL PLGRDGSEPK MQRLGDMTAV 250
    EIKGRIHFDL YHVIRRTINL PTYTLEAVYE AIFGKPKEKV YAHEIAEAWE 300
    TGKGLERVAK YSMEDAKVTY ELGREFFPME AQLSRLVGQP LWDVSRSSTG 350
    NLVEWYLLRK AYERNELAPN KPDEREYERR LRESYAGGYV KEPEKGLWEG 400
    LVSLDFRSLY PSIIITHNVS PDTLNREGCR EYDVAPEVGH KFCKDFPGFI 450
    PSLLKRLLDE RQEIKRKMKA SKDPIEKKML DYRQRAIKIL ANSILPEEWV 500
    PLIKNGKVKI FRIGDFVDGL MKANQGKVKK TGDTEVLEVA GIHAFSFDRK 550
    SKKARVMAVK AVIRHRYSGN VYRIVLNSGR KITITEGHSL FVYRNGDLVE 600
    ATGEDVKIGD LLAVPRSVNL PEKRERLNIV ELLLNLSPEE TEDIILTIPV 650
    KGRKNFFKGM LRTLRWIFGE EKRVRTASRY LRHLENLGYI RLRKIGYDII 700
    DKEGLEKYRT LYEKLVDVVR YNGNKREYLV EFNAVRDVIS LMPEEELKEW 750
    RIGTRNGFRM GTFVDIDEDF AKLLGYYVSE GSARKWKNQT GGWSYTVRLY 800
    NENDEVLDDM EHLAKKFFGK VKRGKNYVEI PKKMAYIIFE SLCGTLAENK 850
    RVPEVIFTSS KGVRWAFLEG YFIGDGDVHP SKRVRLSTKS ELLVNGLVLL 900
    LNSLGVSAIK LGYDSGVYRV YVNEELKFTE YRKKKNVYHS HIVPKDILKE 950
    TFGKVFQKNI SYKKFRELVE NGKLDREKAK RIEWLLNGDI VLDRVVEIKR 1000
    EYYDGYVYDL SVDEDENFLA GFGFLYAHNS YYGYYGYAKA RWYCKECAES 1050
    VTAWGREYIE FVRKELEEKF GFKVLYIDTD GLYATIPGAK PEEIKKKALE 1100
    FVDYINAKLP GLLELEYEGF YVRGFFVTKK KYALIDEEGK IITRGLEIVR 1150
    RDWSEIAKET QAKVLEAILK HGNVEEAVKI VKEVTEKLSK YEIPPEKLVI 1200
    YEQITRPLHE YKAIGPHVAV AKRLAARGVK VRPGMVIGYI VLRGDGPISK 1250
    RAILAEEFDL RKHKYDAEYY IENQVLPAVL RILEAFGYRK EDLRWQKTKQ 1300
    TGLTAWLNIK KK 1312
    Length:1,312
    Mass (Da):152,854
    Last modified:November 1, 1996 - v1
    Checksum:iB62518805641D26A
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00707 Genomic DNA. Translation: AAA67130.1.
    U00707 Genomic DNA. Translation: AAA67131.1.
    U00707 Genomic DNA. Translation: AAA67132.1.
    PIRiS68593.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00707 Genomic DNA. Translation: AAA67130.1 .
    U00707 Genomic DNA. Translation: AAA67131.1 .
    U00707 Genomic DNA. Translation: AAA67132.1 .
    PIRi S68593.

    3D structure databases

    ProteinModelPortali Q51334.
    SMRi Q51334. Positions 1-1310.
    ModBasei Search...
    MobiDBi Search...

    Protein family/group databases

    REBASEi 2619. PI-PspI.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Family and domain databases

    Gene3Di 2.170.16.10. 2 hits.
    3.10.28.10. 2 hits.
    3.30.420.10. 1 hit.
    3.90.1600.10. 2 hits.
    InterProi 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.
    IPR023211. DNA_pol_palm_dom.
    IPR021133. HEAT_type_2.
    IPR028992. Hedgehog/Intein_dom.
    IPR003586. Hint_dom_C.
    IPR003587. Hint_dom_N.
    IPR027434. Homing_endonucl.
    IPR006142. INTEIN.
    IPR004042. Intein_endonuc.
    IPR006141. Intein_splice_site.
    IPR012337. RNaseH-like_dom.
    [Graphical view ]
    Pfami PF00136. DNA_pol_B. 2 hits.
    PF03104. DNA_pol_B_exo1. 2 hits.
    PF14528. LAGLIDADG_3. 1 hit.
    [Graphical view ]
    PRINTSi PR00106. DNAPOLB.
    PR00379. INTEIN.
    SMARTi SM00305. HintC. 1 hit.
    SM00306. HintN. 1 hit.
    SM00486. POLBc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51294. SSF51294. 2 hits.
    SSF53098. SSF53098. 1 hit.
    SSF55608. SSF55608. 1 hit.
    TIGRFAMsi TIGR01443. intein_Cterm. 1 hit.
    TIGR01445. intein_Nterm. 1 hit.
    PROSITEi PS00116. DNA_POLYMERASE_B. 1 hit.
    PS50818. INTEIN_C_TER. 1 hit.
    PS50819. INTEIN_ENDONUCLEASE. 1 hit.
    PS50817. INTEIN_N_TER. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "In vitro protein splicing of purified precursor and the identification of a branched intermediate."
      Xu M.-Q., Southworth M.W., Mersha F.B., Hornstra L.J., Perler F.B.
      Cell 75:1371-1377(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 493-517.

    Entry informationi

    Entry nameiDPOL_PYRSD
    AccessioniPrimary (citable) accession number: Q51334
    Secondary accession number(s): Q51335, Q51336
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1996
    Last modified: October 1, 2014
    This is version 104 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Direct protein sequencing

    Documents

    1. Intein-containing proteins
      List of intein-containing protein entries
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3