DPOL_PYRFU
ID DPOL_PYRFU Reviewed; 775 AA.
AC P61875; P80061; P95584;
DT 07-JUN-2004, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2004, sequence version 1.
DT 25-MAY-2022, entry version 111.
DE RecName: Full=DNA polymerase;
DE EC=2.7.7.7;
DE AltName: Full=DNA polymerase B;
DE AltName: Full=Pfu polymerase;
DE AltName: Full=Pol I;
GN Name=pol; OrderedLocusNames=PF0212;
OS Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=186497;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 1-12.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=8441634; DOI=10.1093/nar/21.2.259;
RA Uemori T., Ishino Y., Toh H., Asada F., Kato I.;
RT "Organization and nucleotide sequence of the DNA polymerase gene from the
RT archaeon Pyrococcus furiosus.";
RL Nucleic Acids Res. 21:259-265(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA DiRuggiero J., Robb F.T.;
RT "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT horikoshii inferred from complete genomic sequences.";
RL Genetics 152:1299-1305(1999).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 396-418.
RX PubMed=1762925; DOI=10.1093/nar/19.24.6952;
RA Mathur E.J., Adams M.W.W., Callen W.N., Cline J.M.;
RT "The DNA polymerase gene from the hyperthermophilic marine archaebacterium,
RT Pyrococcus furiosus, shows sequence homology with alpha-like DNA
RT polymerases.";
RL Nucleic Acids Res. 19:6952-6952(1991).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 396-502.
RA Mathur E.J., Adams M.W.W., Callen W.N., Cline J.M.;
RL Submitted (NOV-1991) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP SIMILARITY TO OTHER POLYMERASES.
RX PubMed=1579479; DOI=10.1093/nar/20.7.1811;
RA Forterre P.;
RT "The DNA polymerase from the archaebacterium Pyrococcus furiosus does not
RT testify for a specific relationship between archaebacteria and
RT eukaryotes.";
RL Nucleic Acids Res. 20:1811-1811(1992).
RN [6]
RP FUNCTION, AND ACTIVITY REGULATION.
RX PubMed=12296822; DOI=10.1046/j.1365-2443.2002.00572.x;
RA Matsumiya S., Ishino S., Ishino Y., Morikawa K.;
RT "Physical interaction between proliferating cell nuclear antigen and
RT replication factor C from Pyrococcus furiosus.";
RL Genes Cells 7:911-922(2002).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), AND SUBUNIT.
RX PubMed=18355915; DOI=10.1016/j.ijbiomac.2008.01.010;
RA Kim S.W., Kim D.U., Kim J.K., Kang L.W., Cho H.S.;
RT "Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus
RT furiosus.";
RL Int. J. Biol. Macromol. 42:356-361(2008).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.67 ANGSTROMS).
RA Nishida H., Mayanagi K., Kiyonari S., Sato Y., Ishino Y., Morikawa K.;
RT "Structural determinant for switching between the polymerase and
RT exonuclease modes in the PCNA-replicative DNA polymerase complex.";
RL Submitted (NOV-2009) to the PDB data bank.
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) WITH AND WITHOUT DNA, BIOTECHNOLOGY,
RP AND DNA-BINDING.
RX PubMed=23940661; DOI=10.1371/journal.pone.0070892;
RA Wynne S.A., Pinheiro V.B., Holliger P., Leslie A.G.;
RT "Structures of an apo and a binary complex of an evolved archeal B family
RT DNA polymerase capable of synthesising highly cy-dye labelled DNA.";
RL PLoS ONE 8:E70892-E70892(2013).
CC -!- FUNCTION: In addition to polymerase activity, this DNA polymerase
CC exhibits 3' to 5' exonuclease activity. {ECO:0000269|PubMed:12296822}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC ChEBI:CHEBI:173112; EC=2.7.7.7;
CC -!- ACTIVITY REGULATION: An 11-mer corresponding to the PIP-box of RfcL
CC inhibits DNA synthesis. {ECO:0000269|PubMed:12296822}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:18355915}.
CC -!- BIOTECHNOLOGY: Because Pfu DNA polymerase exhibits the lowest error
CC rate of any thermostable DNA polymerase studied, it is routinely used
CC for PCR. It is sold by a number of companies including Promega,
CC Stratagene and ThermoScientific. Various mutations to improve its
CC abilities have been incorporated. {ECO:0000269|PubMed:23940661}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-B family. {ECO:0000305}.
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DR EMBL; D12983; BAA02362.1; -; Genomic_DNA.
DR EMBL; AE009950; AAL80336.1; -; Genomic_DNA.
DR PIR; S35543; S35543.
DR RefSeq; WP_011011325.1; NC_018092.1.
DR PDB; 2JGU; X-ray; 2.60 A; A=1-775.
DR PDB; 3A2F; X-ray; 2.67 A; A=1-775.
DR PDB; 4AHC; X-ray; 2.40 A; A/B=1-775.
DR PDB; 4AIL; X-ray; 2.90 A; C=1-775.
DR PDBsum; 2JGU; -.
DR PDBsum; 3A2F; -.
DR PDBsum; 4AHC; -.
DR PDBsum; 4AIL; -.
DR AlphaFoldDB; P61875; -.
DR SMR; P61875; -.
DR STRING; 186497.PF0212; -.
DR EnsemblBacteria; AAL80336; AAL80336; PF0212.
DR GeneID; 41712003; -.
DR KEGG; pfu:PF0212; -.
DR PATRIC; fig|186497.12.peg.220; -.
DR eggNOG; arCOG00328; Archaea.
DR HOGENOM; CLU_000203_6_0_2; -.
DR OMA; GNQKSPY; -.
DR OrthoDB; 35869at2157; -.
DR PhylomeDB; P61875; -.
DR BRENDA; 2.7.7.7; 5243.
DR EvolutionaryTrace; P61875; -.
DR Proteomes; UP000001013; Chromosome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR Gene3D; 1.10.132.60; -; 1.
DR Gene3D; 3.30.420.10; -; 1.
DR Gene3D; 3.90.1600.10; -; 1.
DR IDEAL; IID90009; -.
DR InterPro; IPR006172; DNA-dir_DNA_pol_B.
DR InterPro; IPR017964; DNA-dir_DNA_pol_B_CS.
DR InterPro; IPR006133; DNA-dir_DNA_pol_B_exonuc.
DR InterPro; IPR006134; DNA-dir_DNA_pol_B_multi_dom.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR042087; DNA_pol_B_thumb.
DR InterPro; IPR023211; DNA_pol_palm_dom_sf.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF00136; DNA_pol_B; 1.
DR Pfam; PF03104; DNA_pol_B_exo1; 2.
DR PRINTS; PR00106; DNAPOLB.
DR SMART; SM00486; POLBc; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS00116; DNA_POLYMERASE_B; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; DNA replication; DNA-binding;
KW DNA-directed DNA polymerase; Endonuclease; Hydrolase; Nuclease;
KW Nucleotidyltransferase; Reference proteome; Transferase.
FT CHAIN 1..775
FT /note="DNA polymerase"
FT /id="PRO_0000046480"
FT STRAND 2..10
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 13..22
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 25..31
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 37..43
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 48..52
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 55..58
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 61..64
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 70..75
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 78..86
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 90..92
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 93..100
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 106..111
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 116..124
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 137..144
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:3A2F"
FT STRAND 152..155
FT /evidence="ECO:0007829|PDB:2JGU"
FT STRAND 157..163
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 168..174
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 179..183
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 187..201
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 204..210
FT /evidence="ECO:0007829|PDB:4AHC"
FT TURN 211..214
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 215..225
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 240..246
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 248..251
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 255..259
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 260..267
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 275..283
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 292..301
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 302..304
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 306..337
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 341..344
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 349..363
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 374..382
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 396..408
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 409..416
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 421..423
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 430..434
FT /evidence="ECO:0007829|PDB:4AHC"
FT TURN 436..438
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 441..443
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 449..470
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 474..498
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 508..531
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 536..541
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 544..548
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 554..571
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 578..591
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 594..598
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 604..608
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 610..612
FT /evidence="ECO:0007829|PDB:4AIL"
FT STRAND 614..616
FT /evidence="ECO:0007829|PDB:4AIL"
FT HELIX 620..632
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 637..653
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 658..661
FT /evidence="ECO:0007829|PDB:3A2F"
FT STRAND 663..666
FT /evidence="ECO:0007829|PDB:3A2F"
FT TURN 671..673
FT /evidence="ECO:0007829|PDB:3A2F"
FT TURN 683..687
FT /evidence="ECO:0007829|PDB:4AHC"
FT TURN 689..691
FT /evidence="ECO:0007829|PDB:4AIL"
FT STRAND 696..698
FT /evidence="ECO:0007829|PDB:2JGU"
FT STRAND 702..705
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 706..709
FT /evidence="ECO:0007829|PDB:4AIL"
FT TURN 711..714
FT /evidence="ECO:0007829|PDB:4AHC"
FT STRAND 715..718
FT /evidence="ECO:0007829|PDB:4AHC"
FT TURN 723..725
FT /evidence="ECO:0007829|PDB:3A2F"
FT HELIX 731..735
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 738..746
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 747..749
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 753..756
FT /evidence="ECO:0007829|PDB:4AHC"
FT HELIX 767..769
FT /evidence="ECO:0007829|PDB:3A2F"
SQ SEQUENCE 775 AA; 90113 MW; 5668E3D9F4DBD40E CRC64;
MILDVDYITE EGKPVIRLFK KENGKFKIEH DRTFRPYIYA LLRDDSKIEE VKKITGERHG
KIVRIVDVEK VEKKFLGKPI TVWKLYLEHP QDVPTIREKV REHPAVVDIF EYDIPFAKRY
LIDKGLIPME GEEELKILAF DIETLYHEGE EFGKGPIIMI SYADENEAKV ITWKNIDLPY
VEVVSSEREM IKRFLRIIRE KDPDIIVTYN GDSFDFPYLA KRAEKLGIKL TIGRDGSEPK
MQRIGDMTAV EVKGRIHFDL YHVITRTINL PTYTLEAVYE AIFGKPKEKV YADEIAKAWE
SGENLERVAK YSMEDAKATY ELGKEFLPME IQLSRLVGQP LWDVSRSSTG NLVEWFLLRK
AYERNEVAPN KPSEEEYQRR LRESYTGGFV KEPEKGLWEN IVYLDFRALY PSIIITHNVS
PDTLNLEGCK NYDIAPQVGH KFCKDIPGFI PSLLGHLLEE RQKIKTKMKE TQDPIEKILL
DYRQKAIKLL ANSFYGYYGY AKARWYCKEC AESVTAWGRK YIELVWKELE EKFGFKVLYI
DTDGLYATIP GGESEEIKKK ALEFVKYINS KLPGLLELEY EGFYKRGFFV TKKRYAVIDE
EGKVITRGLE IVRRDWSEIA KETQARVLET ILKHGDVEEA VRIVKEVIQK LANYEIPPEK
LAIYEQITRP LHEYKAIGPH VAVAKKLAAK GVKIKPGMVI GYIVLRGDGP ISNRAILAEE
YDPKKHKYDA EYYIENQVLP AVLRILEGFG YRKEDLRYQK TRQVGLTSWL NIKKS
