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Protein

DNA polymerase

Gene

pol

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.1 Publication

Catalytic activityi

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

Enzyme regulationi

An 11-mer corresponding to the PIP-box of RfcL inhibits DNA synthesis.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

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

Keywords - Biological processi

DNA replication

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BRENDAi2.7.7.7. 5243.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase (EC:2.7.7.7)
Alternative name(s):
DNA polymerase B
Pfu polymerase
Pol I
Gene namesi
Name:pol
Ordered Locus Names:PF0212
OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Taxonomic identifieri186497 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000001013 Componenti: Chromosome

Pathology & Biotechi

Biotechnological usei

Because Pfu DNA polymerase exhibits the lowest error rate of any thermostable DNA polymerase studied, it is routinely used for PCR. It is sold by a number of companies including Promega, Stratagene and ThermoScientific. Various mutations to improve its abilities have been incorporated.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 775775DNA polymerasePRO_0000046480Add
BLAST

Proteomic databases

PRIDEiP61875.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi186497.PF0212.

Structurei

Secondary structure

1
775
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 109Combined sources
Beta strandi13 – 2210Combined sources
Beta strandi25 – 317Combined sources
Beta strandi37 – 437Combined sources
Helixi45 – 473Combined sources
Helixi48 – 525Combined sources
Beta strandi55 – 584Combined sources
Beta strandi61 – 644Combined sources
Beta strandi70 – 756Combined sources
Beta strandi78 – 869Combined sources
Helixi90 – 923Combined sources
Helixi93 – 1008Combined sources
Beta strandi106 – 1116Combined sources
Helixi116 – 1249Combined sources
Beta strandi137 – 1448Combined sources
Beta strandi148 – 1503Combined sources
Beta strandi152 – 1554Combined sources
Beta strandi157 – 1637Combined sources
Beta strandi168 – 1747Combined sources
Beta strandi179 – 1835Combined sources
Helixi187 – 20115Combined sources
Beta strandi204 – 2107Combined sources
Turni211 – 2144Combined sources
Helixi215 – 22511Combined sources
Beta strandi240 – 2467Combined sources
Beta strandi248 – 2514Combined sources
Beta strandi255 – 2595Combined sources
Helixi260 – 2678Combined sources
Helixi275 – 2839Combined sources
Helixi292 – 30110Combined sources
Beta strandi302 – 3043Combined sources
Helixi306 – 33732Combined sources
Helixi341 – 3444Combined sources
Helixi349 – 36315Combined sources
Helixi374 – 3829Combined sources
Beta strandi396 – 40813Combined sources
Helixi409 – 4168Combined sources
Helixi421 – 4233Combined sources
Beta strandi430 – 4345Combined sources
Turni436 – 4383Combined sources
Beta strandi441 – 4433Combined sources
Helixi449 – 47022Combined sources
Helixi474 – 49825Combined sources
Helixi508 – 53124Combined sources
Beta strandi536 – 5416Combined sources
Beta strandi544 – 5485Combined sources
Helixi554 – 57118Combined sources
Beta strandi578 – 59114Combined sources
Beta strandi594 – 5985Combined sources
Beta strandi604 – 6085Combined sources
Helixi610 – 6123Combined sources
Beta strandi614 – 6163Combined sources
Helixi620 – 63213Combined sources
Helixi637 – 65317Combined sources
Helixi658 – 6614Combined sources
Beta strandi663 – 6664Combined sources
Turni671 – 6733Combined sources
Turni683 – 6875Combined sources
Turni689 – 6913Combined sources
Beta strandi696 – 6983Combined sources
Beta strandi702 – 7054Combined sources
Beta strandi706 – 7094Combined sources
Turni711 – 7144Combined sources
Beta strandi715 – 7184Combined sources
Turni723 – 7253Combined sources
Helixi731 – 7355Combined sources
Helixi738 – 7469Combined sources
Helixi747 – 7493Combined sources
Helixi753 – 7564Combined sources
Helixi767 – 7693Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JGUX-ray2.60A1-775[»]
3A2FX-ray2.67A1-775[»]
4AHCX-ray2.40A/B1-775[»]
4AILX-ray2.90C1-775[»]
ProteinModelPortaliP61875.
SMRiP61875. Positions 1-757.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP61875.

Family & Domainsi

Sequence similaritiesi

Belongs to the DNA polymerase type-B family.Curated

Phylogenomic databases

eggNOGiarCOG00328. Archaea.
COG0417. LUCA.
HOGENOMiHOG000222650.
KOiK02319.
OMAiHENVACL.

Family and domain databases

Gene3Di3.30.420.10. 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.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00136. DNA_pol_B. 1 hit.
PF03104. DNA_pol_B_exo1. 2 hits.
[Graphical view]
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P61875-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MILDVDYITE EGKPVIRLFK KENGKFKIEH DRTFRPYIYA LLRDDSKIEE
60 70 80 90 100
VKKITGERHG KIVRIVDVEK VEKKFLGKPI TVWKLYLEHP QDVPTIREKV
110 120 130 140 150
REHPAVVDIF EYDIPFAKRY LIDKGLIPME GEEELKILAF DIETLYHEGE
160 170 180 190 200
EFGKGPIIMI SYADENEAKV ITWKNIDLPY VEVVSSEREM IKRFLRIIRE
210 220 230 240 250
KDPDIIVTYN GDSFDFPYLA KRAEKLGIKL TIGRDGSEPK MQRIGDMTAV
260 270 280 290 300
EVKGRIHFDL YHVITRTINL PTYTLEAVYE AIFGKPKEKV YADEIAKAWE
310 320 330 340 350
SGENLERVAK YSMEDAKATY ELGKEFLPME IQLSRLVGQP LWDVSRSSTG
360 370 380 390 400
NLVEWFLLRK AYERNEVAPN KPSEEEYQRR LRESYTGGFV KEPEKGLWEN
410 420 430 440 450
IVYLDFRALY PSIIITHNVS PDTLNLEGCK NYDIAPQVGH KFCKDIPGFI
460 470 480 490 500
PSLLGHLLEE RQKIKTKMKE TQDPIEKILL DYRQKAIKLL ANSFYGYYGY
510 520 530 540 550
AKARWYCKEC AESVTAWGRK YIELVWKELE EKFGFKVLYI DTDGLYATIP
560 570 580 590 600
GGESEEIKKK ALEFVKYINS KLPGLLELEY EGFYKRGFFV TKKRYAVIDE
610 620 630 640 650
EGKVITRGLE IVRRDWSEIA KETQARVLET ILKHGDVEEA VRIVKEVIQK
660 670 680 690 700
LANYEIPPEK LAIYEQITRP LHEYKAIGPH VAVAKKLAAK GVKIKPGMVI
710 720 730 740 750
GYIVLRGDGP ISNRAILAEE YDPKKHKYDA EYYIENQVLP AVLRILEGFG
760 770
YRKEDLRYQK TRQVGLTSWL NIKKS
Length:775
Mass (Da):90,113
Last modified:June 7, 2004 - v1
Checksum:i5668E3D9F4DBD40E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D12983 Genomic DNA. Translation: BAA02362.1.
AE009950 Genomic DNA. Translation: AAL80336.1.
PIRiS35543.
RefSeqiWP_011011325.1. NC_003413.1.

Genome annotation databases

EnsemblBacteriaiAAL80336; AAL80336; PF0212.
GeneIDi1468044.
KEGGipfu:PF0212.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D12983 Genomic DNA. Translation: BAA02362.1.
AE009950 Genomic DNA. Translation: AAL80336.1.
PIRiS35543.
RefSeqiWP_011011325.1. NC_003413.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JGUX-ray2.60A1-775[»]
3A2FX-ray2.67A1-775[»]
4AHCX-ray2.40A/B1-775[»]
4AILX-ray2.90C1-775[»]
ProteinModelPortaliP61875.
SMRiP61875. Positions 1-757.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi186497.PF0212.

Proteomic databases

PRIDEiP61875.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL80336; AAL80336; PF0212.
GeneIDi1468044.
KEGGipfu:PF0212.

Phylogenomic databases

eggNOGiarCOG00328. Archaea.
COG0417. LUCA.
HOGENOMiHOG000222650.
KOiK02319.
OMAiHENVACL.

Enzyme and pathway databases

BRENDAi2.7.7.7. 5243.

Miscellaneous databases

EvolutionaryTraceiP61875.

Family and domain databases

Gene3Di3.30.420.10. 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.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00136. DNA_pol_B. 1 hit.
PF03104. DNA_pol_B_exo1. 2 hits.
[Graphical view]
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Organization and nucleotide sequence of the DNA polymerase gene from the archaeon Pyrococcus furiosus."
    Uemori T., Ishino Y., Toh H., Asada F., Kato I.
    Nucleic Acids Res. 21:259-265(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-12.
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
  2. "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
    Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
    Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
  3. "The DNA polymerase gene from the hyperthermophilic marine archaebacterium, Pyrococcus furiosus, shows sequence homology with alpha-like DNA polymerases."
    Mathur E.J., Adams M.W.W., Callen W.N., Cline J.M.
    Nucleic Acids Res. 19:6952-6952(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 396-418.
  4. Mathur E.J., Adams M.W.W., Callen W.N., Cline J.M.
    Submitted (NOV-1991) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 396-502.
  5. "The DNA polymerase from the archaebacterium Pyrococcus furiosus does not testify for a specific relationship between archaebacteria and eukaryotes."
    Forterre P.
    Nucleic Acids Res. 20:1811-1811(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: SIMILARITY TO OTHER POLYMERASES.
  6. "Physical interaction between proliferating cell nuclear antigen and replication factor C from Pyrococcus furiosus."
    Matsumiya S., Ishino S., Ishino Y., Morikawa K.
    Genes Cells 7:911-922(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION.
  7. "Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus."
    Kim S.W., Kim D.U., Kim J.K., Kang L.W., Cho H.S.
    Int. J. Biol. Macromol. 42:356-361(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), SUBUNIT.
  8. "Structural determinant for switching between the polymerase and exonuclease modes in the PCNA-replicative DNA polymerase complex."
    Nishida H., Mayanagi K., Kiyonari S., Sato Y., Ishino Y., Morikawa K.
    Submitted (NOV-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.67 ANGSTROMS).
  9. "Structures of an apo and a binary complex of an evolved archeal B family DNA polymerase capable of synthesising highly cy-dye labelled DNA."
    Wynne S.A., Pinheiro V.B., Holliger P., Leslie A.G.
    PLoS ONE 8:E70892-E70892(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) WITH AND WITHOUT DNA, BIOTECHNOLOGY, DNA-BINDING.

Entry informationi

Entry nameiDPOL_PYRFU
AccessioniPrimary (citable) accession number: P61875
Secondary accession number(s): P80061, P95584
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2004
Last sequence update: June 7, 2004
Last modified: November 11, 2015
This is version 81 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, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.