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Q9V2F4

- DP2L_PYRAB

UniProt

Q9V2F4 - DP2L_PYRAB

Protein

DNA polymerase II large subunit

Gene

polC

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 89 (01 Oct 2014)
      Sequence version 1 (01 May 2000)
      Previous versions | rss
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    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

    Catalytic activityi

    Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    Degradation of single-stranded DNA. It acts progressively in a 3'- to 5'-direction, releasing nucleoside 5'-phosphates.

    GO - Molecular functioni

    1. 3'-5' exonuclease activity Source: UniProtKB-HAMAP
    2. DNA binding Source: UniProtKB-HAMAP
    3. DNA-directed DNA polymerase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. DNA catabolic process, exonucleolytic Source: UniProtKB-HAMAP
    2. intein-mediated protein splicing Source: InterPro

    Keywords - Molecular functioni

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

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    DNA-binding

    Protein family/group databases

    MEROPSiN10.005.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA polymerase II large subunit (EC:2.7.7.7)
    Short name:
    Pol II
    Cleaved into the following chain:
    Alternative name(s):
    Pab pol II intein
    Gene namesi
    Name:polC
    Ordered Locus Names:PYRAB01200
    ORF Names:PAB2404
    OrganismiPyrococcus abyssi (strain GE5 / Orsay)
    Taxonomic identifieri272844 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
    ProteomesiUP000000810: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 954954DNA polymerase II large subunit, 1st partSequence AnalysisPRO_0000007304Add
    BLAST
    Chaini955 – 1139185Pab polC inteinSequence AnalysisPRO_0000007305Add
    BLAST
    Chaini1140 – 1455316DNA polymerase II large subunit, 2nd partSequence AnalysisPRO_0000007306Add
    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.Curated

    Keywords - PTMi

    Autocatalytic cleavage, Protein splicing

    Interactioni

    Subunit structurei

    Heterodimer of a large subunit and a small subunit.By similarity

    Protein-protein interaction databases

    STRINGi272844.PAB2404.

    Structurei

    Secondary structure

    1
    1455
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi960 – 9667
    Beta strandi969 – 9746
    Helixi975 – 9784
    Helixi979 – 9813
    Beta strandi985 – 9884
    Beta strandi991 – 9944
    Beta strandi996 – 9994
    Beta strandi1001 – 10077
    Turni1008 – 10114
    Beta strandi1012 – 102514
    Beta strandi1030 – 10356
    Beta strandi1040 – 10434
    Beta strandi1045 – 10539
    Beta strandi1056 – 10616
    Helixi1062 – 10643
    Beta strandi1070 – 10734
    Beta strandi1083 – 10864
    Beta strandi1103 – 11119
    Beta strandi1114 – 11196
    Beta strandi1126 – 11316
    Turni1132 – 11343
    Beta strandi1135 – 11384

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2LCJNMR-A955-1139[»]
    ProteinModelPortaliQ9V2F4.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the archaeal DNA polymerase II family.Curated

    Phylogenomic databases

    eggNOGiCOG1933.
    HOGENOMiHOG000286435.
    KOiK02322.
    OMAiRNCDGDE.

    Family and domain databases

    Gene3Di2.170.16.10. 1 hit.
    HAMAPiMF_00324. DNApol_II_L_arch.
    InterProiIPR028992. Hedgehog/Intein_dom.
    IPR003587. Hint_dom_N.
    IPR006141. Intein_splice_site.
    IPR004475. PolC_DP2.
    IPR016033. PolC_DP2_N.
    [Graphical view]
    PfamiPF03833. PolC_DP2. 1 hit.
    [Graphical view]
    SMARTiSM00306. HintN. 1 hit.
    [Graphical view]
    SUPFAMiSSF51294. SSF51294. 1 hit.
    TIGRFAMsiTIGR01445. intein_Nterm. 1 hit.
    TIGR00354. polC. 1 hit.
    PROSITEiPS50818. INTEIN_C_TER. 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.

    Q9V2F4-1 [UniParc]FASTAAdd to Basket

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    MELPKEMEEY FEMLQREIDK AYEIAKKARA QGKDPSLDVE IPQATDMAGR     50
    VESLVGPPGV AKRIRELVKE YGKEIAALKI VDEIIEGKFG DLGSREKYAE 100
    QAVRTALAIL TEGIVSAPIE GIANVKIKRN TWADNSEYLA LYYAGPIRSS 150
    GGTAQALSVL VGDYVRRKLG LDRFKPSEKH IERMVEEVDL YHRAVTRLQY 200
    HPSPEEVRLA MRNIPIEITG EATDDVEVSH RDVPGVETNQ LRGGAILVLA 250
    EGVLQKAKKL VKYIDKMGIE GWEWLKEFVE AKEKGEPKEE GKEESLAEST 300
    LEETKVEVDM GFYYSLYQKF KEEIAPSDKY AKEVIGGRPL FSDPSKPGGF 350
    RLRYGRSRAS GFATWGINPA TMILVDEFLA IGTQLKTERP GKGAVVTPVT 400
    TIEGPIVKLK DGSVLRVDDY NLALKVREDV EEILYLGDAV IAFGDFVENN 450
    QTLLPANYCE EWWILEFVKA LKEIYEVHLE PFTENEEESI EEASDYLEID 500
    PEFLKEMLRD PLRVKPPVEL AIHFSEVLGI PLHPYYTLYW NSVEPKDVEK 550
    LWRLLKNYAE IEWSNFRGIK FAKKIVISQE KLGDSKRTLE LLGLPHTVRD 600
    GNVIVDYPWA AALLTPLGNL NWEFMAKPLY ATIDIINENN EIKLRDRGIS 650
    WIGARMGRPE KAKERKMKPP VQVLFPIGLA GGSSRDIKKA AEEGKVAEVE 700
    IAFFKCPKCG HVGPEHLCPN CGTRKELLWV CPRCNAEYPE SQAEGYNYTC 750
    PKCNVKLRPY AKRKIRPSEL LNRAMENVKV YGVDKLKGVM GMTSGWKMPE 800
    PLEKGLLRAK NDVYVFKDGT IRFDATDAPI THFRPREIGV SVEKLRELGY 850
    THDFEGKPLV SEDQIVELKP QDIILSKEAG RYLLKVAKFV DDLLEKFYGL 900
    PRFYNAEKME DLIGHLVIGL APHTSAGIVG RIIGFVDALV GYAHPYFHAA 950
    KRRNCFPGDT RILVQIDGVP QKITLRELYE LFEDERYENM VYVRKKPKRE 1000
    IKVYSIDLET GKVVLTDIED VIKAPATDHL IRFELEDGRS FETTVDHPVL 1050
    VYENGRFIEK RAFEVKEGDK VLVSELELVE QSSSSQDNPK NENLGSPEHD 1100
    QLLEIKNIKY VRANDDFVFS LNAKKYHNVI INENIVTHQC DGDEDAVMLL 1150
    LDALLNFSRY YLPEKRGGKM DAPLVITTRL DPREVDSEVH NMDIVRYYPL 1200
    EFYEATYELK SPKELVGVIE RVEDRLGKPE MYYGLKFTHD TDDIALGPKM 1250
    SLYKQLGDME EKVRRQLEVA KRIRAVDEHG VAEKILNSHL IPDLRGNLRS 1300
    FTRQEFRCVK CNTKFRRPPL NGKCPVCGGK IVLTVSKGAI EKYLGTAKML 1350
    VTEYNVKNYT RQRICLTERD IDSLFENVFP ETQLTLIVNP NDICQRLVMA 1400
    RTGEVNKSGL LENLSNGSKK TEKAEKAEKP RKKSDEKPKK KRVISLEEFF 1450
    SRKSK 1455
    Length:1,455
    Mass (Da):165,711
    Last modified:May 1, 2000 - v1
    Checksum:iBB092E7BB2FE0D21
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ248283 Genomic DNA. Translation: CAB49044.1.
    HE613800 Genomic DNA. Translation: CCE69496.1.
    PIRiE75199.
    RefSeqiNP_125813.1. NC_000868.1.

    Genome annotation databases

    EnsemblBacteriaiCAB49044; CAB49044; PAB2404.
    GeneIDi1495007.
    KEGGipab:PAB2404.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ248283 Genomic DNA. Translation: CAB49044.1 .
    HE613800 Genomic DNA. Translation: CCE69496.1 .
    PIRi E75199.
    RefSeqi NP_125813.1. NC_000868.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2LCJ NMR - A 955-1139 [» ]
    ProteinModelPortali Q9V2F4.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 272844.PAB2404.

    Protein family/group databases

    MEROPSi N10.005.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB49044 ; CAB49044 ; PAB2404 .
    GeneIDi 1495007.
    KEGGi pab:PAB2404.

    Phylogenomic databases

    eggNOGi COG1933.
    HOGENOMi HOG000286435.
    KOi K02322.
    OMAi RNCDGDE.

    Family and domain databases

    Gene3Di 2.170.16.10. 1 hit.
    HAMAPi MF_00324. DNApol_II_L_arch.
    InterProi IPR028992. Hedgehog/Intein_dom.
    IPR003587. Hint_dom_N.
    IPR006141. Intein_splice_site.
    IPR004475. PolC_DP2.
    IPR016033. PolC_DP2_N.
    [Graphical view ]
    Pfami PF03833. PolC_DP2. 1 hit.
    [Graphical view ]
    SMARTi SM00306. HintN. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51294. SSF51294. 1 hit.
    TIGRFAMsi TIGR01445. intein_Nterm. 1 hit.
    TIGR00354. polC. 1 hit.
    PROSITEi PS50818. INTEIN_C_TER. 1 hit.
    PS50817. INTEIN_N_TER. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: GE5 / Orsay.
    2. "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638."
      Gao J., Wang J.
      Curr. Microbiol. 64:118-129(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENOME REANNOTATION.
      Strain: GE5 / Orsay.

    Entry informationi

    Entry nameiDP2L_PYRAB
    AccessioniPrimary (citable) accession number: Q9V2F4
    Secondary accession number(s): G8ZFV5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 27, 2001
    Last sequence update: May 1, 2000
    Last modified: October 1, 2014
    This is version 89 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

    3D-structure, Complete proteome, Multifunctional enzyme

    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

    External Data

    Dasty 3