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P77933

- DPOL_THEKO

UniProt

P77933 - DPOL_THEKO

Protein

DNA polymerase

Gene

pol

Organism
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 132 (01 Oct 2014)
      Sequence version 3 (29 Mar 2005)
      Previous versions | rss
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    Functioni

    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. PI-PkoI recognizes 5'-GATTTAGATCCCTGTACC-3' and PI-PkoII recognizes 5'-CAGCTACTACGGTTAC-3'.

    Catalytic activityi

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

    Temperature dependencei

    Thermostable.

    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

    Enzyme and pathway databases

    BioCyciTKOD69014:GH72-1-MONOMER.

    Protein family/group databases

    MEROPSiN10.007.
    REBASEi3792. PI-PkoI.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA polymerase (EC:2.7.7.7)
    Cleaved into the following 2 chains:
    Alternative name(s):
    IVS-A
    Pko pol-1 intein
    Alternative name(s):
    IVS-B
    Pko pol-2 intein
    Gene namesi
    Name:pol
    Ordered Locus Names:TK0001
    OrganismiThermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
    Taxonomic identifieri69014 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
    ProteomesiUP000000536: Chromosome

    Pathology & Biotechi

    Biotechnological usei

    Pyrococcus kodakaraensis enzyme is the fastest thermostable DNA polymerase known today (130 nucleotides/s) and is used in high-performance PCR.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 406406DNA polymerase, 1st partPRO_0000007325Add
    BLAST
    Chaini407 – 766360Endonuclease PI-PkoIPRO_0000007326Add
    BLAST
    Chaini767 – 85185DNA polymerase, 2nd partPRO_0000007327Add
    BLAST
    Chaini852 – 1388537Endonuclease PI-PkoIIPRO_0000007328Add
    BLAST
    Chaini1389 – 1671283DNA polymerase, 3rd partPRO_0000007329Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi788 ↔ 802
    Disulfide bondi1403 ↔ 1406

    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, Disulfide bond, Protein splicing

    Interactioni

    Protein-protein interaction databases

    STRINGi69014.TK0001.

    Structurei

    Secondary structure

    1
    1671
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 105
    Beta strandi13 – 208
    Beta strandi23 – 253
    Beta strandi27 – 315
    Beta strandi37 – 437
    Turni45 – 473
    Helixi48 – 514
    Beta strandi56 – 583
    Beta strandi61 – 633
    Beta strandi68 – 758
    Beta strandi78 – 869
    Helixi90 – 956
    Helixi97 – 1026
    Beta strandi106 – 1116
    Helixi116 – 1238
    Beta strandi137 – 1448
    Beta strandi157 – 1626
    Turni164 – 1663
    Beta strandi169 – 1746
    Beta strandi181 – 1833
    Helixi187 – 20115
    Beta strandi204 – 2107
    Turni211 – 2144
    Helixi215 – 22410
    Turni225 – 2273
    Beta strandi241 – 2444
    Beta strandi247 – 2504
    Beta strandi255 – 2595
    Helixi260 – 2678
    Helixi275 – 2839
    Helixi292 – 3009
    Helixi305 – 33733
    Helixi341 – 3444
    Helixi349 – 36315
    Helixi374 – 3807
    Beta strandi395 – 40511
    Helixi768 – 7769
    Turni780 – 7823
    Beta strandi791 – 7933
    Turni795 – 7973
    Beta strandi800 – 8023
    Helixi808 – 82821
    Helixi833 – 85018
    Beta strandi858 – 8636
    Beta strandi866 – 8716
    Helixi872 – 88110
    Helixi884 – 8863
    Beta strandi888 – 8903
    Beta strandi893 – 8975
    Beta strandi900 – 9067
    Turni908 – 9103
    Beta strandi913 – 93523
    Beta strandi940 – 9445
    Beta strandi948 – 9536
    Beta strandi956 – 9616
    Turni962 – 9643
    Beta strandi970 – 9756
    Beta strandi985 – 9873
    Helixi988 – 9936
    Helixi997 – 9993
    Beta strandi1004 – 10118
    Helixi1015 – 102612
    Helixi1036 – 104611
    Beta strandi1048 – 10514
    Beta strandi1053 – 10597
    Helixi1061 – 107717
    Beta strandi1079 – 10813
    Turni1082 – 10843
    Beta strandi1085 – 10884
    Helixi1091 – 10944
    Helixi1095 – 10984
    Helixi1103 – 11064
    Beta strandi1110 – 11123
    Beta strandi1118 – 11247
    Helixi1127 – 113913
    Beta strandi1140 – 11456
    Turni1147 – 11504
    Beta strandi1153 – 11597
    Helixi1163 – 117715
    Beta strandi1184 – 11896
    Helixi1192 – 120211
    Helixi1206 – 12083
    Helixi1213 – 12153
    Helixi1220 – 123415
    Beta strandi1240 – 12489
    Helixi1250 – 126213
    Beta strandi1268 – 12725
    Beta strandi1277 – 12815
    Turni1292 – 12954
    Helixi1298 – 13003
    Helixi1304 – 13118
    Helixi1321 – 13299
    Helixi1335 – 13384
    Helixi1339 – 13413
    Helixi1342 – 13465
    Beta strandi1347 – 137125
    Turni1372 – 13743
    Beta strandi1376 – 13794
    Beta strandi1384 – 13874
    Helixi1390 – 13945
    Helixi1404 – 142623
    Turni1427 – 14293
    Beta strandi1435 – 14373
    Beta strandi1440 – 14434
    Helixi1450 – 146718
    Beta strandi1478 – 14858
    Beta strandi1491 – 14944
    Helixi1517 – 152711
    Turni1528 – 15303
    Helixi1534 – 15418
    Turni1542 – 15509
    Helixi1555 – 15573
    Turni1577 – 15826
    Beta strandi1614 – 16174
    Beta strandi1620 – 16223
    Helixi1630 – 16345
    Helixi1635 – 16417
    Helixi1649 – 16535

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1WN7X-ray2.75A1-810[»]
    1WNSX-ray3.00A1-1671[»]
    2CW7X-ray2.70A852-1388[»]
    2CW8X-ray2.50A852-1388[»]
    ProteinModelPortaliP77933.
    SMRiP77933. Positions 1-406, 763-1669.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP77933.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini524 – 665142DOD-type homing endonuclease 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini1132 – 1265134DOD-type homing endonuclease 2PROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni135 – 3261923'-5' exonucleaseAdd
    BLAST

    Sequence similaritiesi

    Belongs to the DNA polymerase type-B family.Curated
    Contains 2 DOD-type homing endonuclease domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiCOG0417.
    HOGENOMiHOG000222650.
    KOiK02319.

    Family and domain databases

    Gene3Di2.170.16.10. 3 hits.
    3.10.28.10. 3 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.
    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. 3 hits.
    PF03104. DNA_pol_B_exo1. 2 hits.
    PF14528. LAGLIDADG_3. 2 hits.
    [Graphical view]
    PRINTSiPR00379. INTEIN.
    SMARTiSM00305. HintC. 2 hits.
    SM00306. HintN. 2 hits.
    SM00486. POLBc. 1 hit.
    [Graphical view]
    SUPFAMiSSF51294. SSF51294. 4 hits.
    SSF53098. SSF53098. 1 hit.
    SSF55608. SSF55608. 2 hits.
    TIGRFAMsiTIGR01443. intein_Cterm. 2 hits.
    TIGR01445. intein_Nterm. 1 hit.
    PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
    PS50818. INTEIN_C_TER. 2 hits.
    PS50819. INTEIN_ENDONUCLEASE. 2 hits.
    PS50817. INTEIN_N_TER. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P77933-1 [UniParc]FASTAAdd to Basket

    « Hide

    MILDTDYITE DGKPVIRIFK KENGEFKIEY DRTFEPYFYA LLKDDSAIEE     50
    VKKITAERHG TVVTVKRVEK VQKKFLGRPV EVWKLYFTHP QDVPAIRDKI 100
    REHPAVIDIY EYDIPFAKRY LIDKGLVPME GDEELKMLAF DIETLYHEGE 150
    EFAEGPILMI SYADEEGARV ITWKNVDLPY VDVVSTEREM IKRFLRVVKE 200
    KDPDVLITYN GDNFDFAYLK KRCEKLGINF ALGRDGSEPK IQRMGDRFAV 250
    EVKGRIHFDL YPVIRRTINL PTYTLEAVYE AVFGQPKEKV YAEEITTAWE 300
    TGENLERVAR YSMEDAKVTY ELGKEFLPME AQLSRLIGQS LWDVSRSSTG 350
    NLVEWFLLRK AYERNELAPN KPDEKELARR RQSYEGGYVK EPERGLWENI 400
    VYLDFRCHPA DTKVVVKGKG IINISEVQEG DYVLGIDGWQ RVRKVWEYDY 450
    KGELVNINGL KCTPNHKLPV VTKNERQTRI RDSLAKSFLT KKVKGKIITT 500
    PLFYEIGRAT SENIPEEEVL KGELAGILLA EGTLLRKDVE YFDSSRKKRR 550
    ISHQYRVEIT IGKDEEEFRD RITYIFERLF GITPSISEKK GTNAVTLKVA 600
    KKNVYLKVKE IMDNIESLHA PSVLRGFFEG DGSVNRVRRS IVATQGTKNE 650
    WKIKLVSKLL SQLGIPHQTY TYQYQENGKD RSRYILEITG KDGLILFQTL 700
    IGFISERKNA LLNKAISQRE MNNLENNGFY RLSEFNVSTE YYEGKVYDLT 750
    LEGTPYYFAN GILTHNSLYP SIIITHNVSP DTLNREGCKE YDVAPQVGHR 800
    FCKDFPGFIP SLLGDLLEER QKIKKKMKAT IDPIERKLLD YRQRAIKILA 850
    NSILPEEWLP VLEEGEVHFV RIGELIDRMM EENAGKVKRE GETEVLEVSG 900
    LEVPSFNRRT KKAELKRVKA LIRHDYSGKV YTIRLKSGRR IKITSGHSLF 950
    SVRNGELVEV TGDELKPGDL VAVPRRLELP ERNHVLNLVE LLLGTPEEET 1000
    LDIVMTIPVK GKKNFFKGML RTLRWIFGEE KRPRTARRYL RHLEDLGYVR 1050
    LKKIGYEVLD WDSLKNYRRL YEALVENVRY NGNKREYLVE FNSIRDAVGI 1100
    MPLKELKEWK IGTLNGFRMS PLIEVDESLA KLLGYYVSEG YARKQRNPKN 1150
    GWSYSVKLYN EDPEVLDDME RLASRFFGKV RRGRNYVEIP KKIGYLLFEN 1200
    MCGVLAENKR IPEFVFTSPK GVRLAFLEGY FIGDGDVHPN KRLRLSTKSE 1250
    LLANQLVLLL NSVGVSAVKL GHDSGVYRVY INEELPFVKL DKKKNAYYSH 1300
    VIPKEVLSEV FGKVFQKNVS PQTFRKMVED GRLDPEKAQR LSWLIEGDVV 1350
    LDRVESVDVE DYDGYVYDLS VEDNENFLVG FGLVYAHNSY YGYYGYARAR 1400
    WYCKECAESV TAWGREYITM TIKEIEEKYG FKVIYSDTDG FFATIPGADA 1450
    ETVKKKAMEF LKYINAKLPG ALELEYEGFY KRGFFVTKKK YAVIDEEGKI 1500
    TTRGLEIVRR DWSEIAKETQ ARVLEALLKD GDVEKAVRIV KEVTEKLSKY 1550
    EVPPEKLVIH EQITRDLKDY KATGPHVAVA KRLAARGVKI RPGTVISYIV 1600
    LKGSGRIGDR AIPFDEFDPT KHKYDAEYYI ENQVLPAVER ILRAFGYRKE 1650
    DLRYQKTRQV GLSAWLKPKG T 1671
    Length:1,671
    Mass (Da):193,405
    Last modified:March 29, 2005 - v3
    Checksum:iD9C0029BE7EE2203
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti911 – 9111K → N in BAA06142. (PubMed:9361436)Curated
    Sequence conflicti1120 – 11212SP → RK in BAA06142. (PubMed:9361436)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D29671 Genomic DNA. Translation: BAA06142.2.
    AP006878 Genomic DNA. Translation: BAD84190.1.
    PIRiS71551.
    RefSeqiYP_182414.1. NC_006624.1.

    Genome annotation databases

    EnsemblBacteriaiBAD84190; BAD84190; TK0001.
    GeneIDi3233723.
    KEGGitko:TK0001.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D29671 Genomic DNA. Translation: BAA06142.2 .
    AP006878 Genomic DNA. Translation: BAD84190.1 .
    PIRi S71551.
    RefSeqi YP_182414.1. NC_006624.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1WN7 X-ray 2.75 A 1-810 [» ]
    1WNS X-ray 3.00 A 1-1671 [» ]
    2CW7 X-ray 2.70 A 852-1388 [» ]
    2CW8 X-ray 2.50 A 852-1388 [» ]
    ProteinModelPortali P77933.
    SMRi P77933. Positions 1-406, 763-1669.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 69014.TK0001.

    Protein family/group databases

    MEROPSi N10.007.
    REBASEi 3792. PI-PkoI.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAD84190 ; BAD84190 ; TK0001 .
    GeneIDi 3233723.
    KEGGi tko:TK0001.

    Phylogenomic databases

    eggNOGi COG0417.
    HOGENOMi HOG000222650.
    KOi K02319.

    Enzyme and pathway databases

    BioCyci TKOD69014:GH72-1-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P77933.

    Family and domain databases

    Gene3Di 2.170.16.10. 3 hits.
    3.10.28.10. 3 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.
    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. 3 hits.
    PF03104. DNA_pol_B_exo1. 2 hits.
    PF14528. LAGLIDADG_3. 2 hits.
    [Graphical view ]
    PRINTSi PR00379. INTEIN.
    SMARTi SM00305. HintC. 2 hits.
    SM00306. HintN. 2 hits.
    SM00486. POLBc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51294. SSF51294. 4 hits.
    SSF53098. SSF53098. 1 hit.
    SSF55608. SSF55608. 2 hits.
    TIGRFAMsi TIGR01443. intein_Cterm. 2 hits.
    TIGR01445. intein_Nterm. 1 hit.
    PROSITEi PS00116. DNA_POLYMERASE_B. 1 hit.
    PS50818. INTEIN_C_TER. 2 hits.
    PS50819. INTEIN_ENDONUCLEASE. 2 hits.
    PS50817. INTEIN_N_TER. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR."
      Takagi M., Nishioka M., Kakihara H., Kitabayashi M., Inoue H., Kawakami B., Oka M., Imanaka T.
      Appl. Environ. Microbiol. 63:4504-4510(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    2. "Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes."
      Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.
      Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    3. "Characterization of two intein homing endonucleases encoded in the DNA polymerase gene of Pyrococcus kodakaraensis strain KOD1."
      Nishioka M., Fujiwara S., Takagi M., Imanaka T.
      Nucleic Acids Res. 26:4409-4412(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION OF INTEINS.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    4. "Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1."
      Hashimoto H., Nishioka M., Fujiwara S., Takagi M., Imanaka T., Inoue T., Kai Y.
      J. Mol. Biol. 306:469-477(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF DNA POLYMERASE.

    Entry informationi

    Entry nameiDPOL_THEKO
    AccessioniPrimary (citable) accession number: P77933
    Secondary accession number(s): Q5JEA7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 27, 2001
    Last sequence update: March 29, 2005
    Last modified: October 1, 2014
    This is version 132 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    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