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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)DescriptionActionsGraphical viewLength
ChainiPRO_00000464801 – 775DNA polymeraseAdd BLAST775

Proteomic databases

PRIDEiP61875.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi186497.PF0212.

Structurei

Secondary structure

1775
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 10Combined sources9
Beta strandi13 – 22Combined sources10
Beta strandi25 – 31Combined sources7
Beta strandi37 – 43Combined sources7
Helixi45 – 47Combined sources3
Helixi48 – 52Combined sources5
Beta strandi55 – 58Combined sources4
Beta strandi61 – 64Combined sources4
Beta strandi70 – 75Combined sources6
Beta strandi78 – 86Combined sources9
Helixi90 – 92Combined sources3
Helixi93 – 100Combined sources8
Beta strandi106 – 111Combined sources6
Helixi116 – 124Combined sources9
Beta strandi137 – 144Combined sources8
Beta strandi148 – 150Combined sources3
Beta strandi152 – 155Combined sources4
Beta strandi157 – 163Combined sources7
Beta strandi168 – 174Combined sources7
Beta strandi179 – 183Combined sources5
Helixi187 – 201Combined sources15
Beta strandi204 – 210Combined sources7
Turni211 – 214Combined sources4
Helixi215 – 225Combined sources11
Beta strandi240 – 246Combined sources7
Beta strandi248 – 251Combined sources4
Beta strandi255 – 259Combined sources5
Helixi260 – 267Combined sources8
Helixi275 – 283Combined sources9
Helixi292 – 301Combined sources10
Beta strandi302 – 304Combined sources3
Helixi306 – 337Combined sources32
Helixi341 – 344Combined sources4
Helixi349 – 363Combined sources15
Helixi374 – 382Combined sources9
Beta strandi396 – 408Combined sources13
Helixi409 – 416Combined sources8
Helixi421 – 423Combined sources3
Beta strandi430 – 434Combined sources5
Turni436 – 438Combined sources3
Beta strandi441 – 443Combined sources3
Helixi449 – 470Combined sources22
Helixi474 – 498Combined sources25
Helixi508 – 531Combined sources24
Beta strandi536 – 541Combined sources6
Beta strandi544 – 548Combined sources5
Helixi554 – 571Combined sources18
Beta strandi578 – 591Combined sources14
Beta strandi594 – 598Combined sources5
Beta strandi604 – 608Combined sources5
Helixi610 – 612Combined sources3
Beta strandi614 – 616Combined sources3
Helixi620 – 632Combined sources13
Helixi637 – 653Combined sources17
Helixi658 – 661Combined sources4
Beta strandi663 – 666Combined sources4
Turni671 – 673Combined sources3
Turni683 – 687Combined sources5
Turni689 – 691Combined sources3
Beta strandi696 – 698Combined sources3
Beta strandi702 – 705Combined sources4
Beta strandi706 – 709Combined sources4
Turni711 – 714Combined sources4
Beta strandi715 – 718Combined sources4
Turni723 – 725Combined sources3
Helixi731 – 735Combined sources5
Helixi738 – 746Combined sources9
Helixi747 – 749Combined sources3
Helixi753 – 756Combined sources4
Helixi767 – 769Combined sources3

3D structure databases

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

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2JGUX-ray2.60A1-775[»]
3A2FX-ray2.67A1-775[»]
4AHCX-ray2.40A/B1-775[»]
4AILX-ray2.90C1-775[»]
ProteinModelPortaliP61875.
SMRiP61875.
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.
OMAiDIPFAYR.

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...

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 2, 2016
This is version 84 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.