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Protein

DNA polymerase

Gene

pol

Organism
Pyrococcus sp. (strain GB-D)
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.
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.

Catalytic activityi

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

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. DNA replication Source: UniProtKB-KW
  2. intein-mediated protein splicing Source: InterPro
  3. intron homing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

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

Keywords - Biological processi

DNA replication, Intron homing

Keywords - Ligandi

DNA-binding

Protein family/group databases

MEROPSiN10.007.
REBASEi2619. PI-PspI.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase (EC:2.7.7.7)
Alternative name(s):
Deep vent DNA polymerase
Cleaved into the following chain:
Alternative name(s):
Psp-GDB pol intein
Gene namesi
Name:pol
OrganismiPyrococcus sp. (strain GB-D)
Taxonomic identifieri69013 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus

Pathology & Biotechi

Biotechnological usei

Used in the PCR method because of its high thermostability and low error rate. Sold by New England Biolabs.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 492492DNA polymerase, 1st partPRO_0000007330Add
BLAST
Chaini493 – 1029537Endonuclease PI-PspIPRO_0000007331Add
BLAST
Chaini1030 – 1312283DNA polymerase, 2nd partPRO_0000007332Add
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.

Keywords - PTMi

Autocatalytic cleavage, Protein splicing

Structurei

3D structure databases

ProteinModelPortaliQ51334.
SMRiQ51334. Positions 1-1310.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini773 – 906134DOD-type homing endonucleasePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the DNA polymerase type-B family.Curated
Contains 1 DOD-type homing endonuclease domain.PROSITE-ProRule annotation

Family and domain databases

Gene3Di2.170.16.10. 2 hits.
3.10.28.10. 2 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.
IPR021133. HEAT_type_2.
IPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00136. DNA_pol_B. 2 hits.
PF03104. DNA_pol_B_exo1. 2 hits.
PF14528. LAGLIDADG_3. 1 hit.
[Graphical view]
PRINTSiPR00106. DNAPOLB.
PR00379. INTEIN.
SMARTiSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF51294. SSF51294. 2 hits.
SSF53098. SSF53098. 1 hit.
SSF55608. SSF55608. 1 hit.
TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
PS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 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.

Q51334-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MILDADYITE DGKPIIRIFK KENGEFKVEY DRNFRPYIYA LLKDDSQIDE
60 70 80 90 100
VRKITAERHG KIVRIIDAEK VRKKFLGRPI EVWRLYFEHP QDVPAIRDKI
110 120 130 140 150
REHSAVIDIF EYDIPFAKRY LIDKGLIPME GDEELKLLAF DIETLYHEGE
160 170 180 190 200
EFAKGPIIMI SYADEEEAKV ITWKKIDLPY VEVVSSEREM IKRFLKVIRE
210 220 230 240 250
KDPDVIITYN GDSFDLPYLV KRAEKLGIKL PLGRDGSEPK MQRLGDMTAV
260 270 280 290 300
EIKGRIHFDL YHVIRRTINL PTYTLEAVYE AIFGKPKEKV YAHEIAEAWE
310 320 330 340 350
TGKGLERVAK YSMEDAKVTY ELGREFFPME AQLSRLVGQP LWDVSRSSTG
360 370 380 390 400
NLVEWYLLRK AYERNELAPN KPDEREYERR LRESYAGGYV KEPEKGLWEG
410 420 430 440 450
LVSLDFRSLY PSIIITHNVS PDTLNREGCR EYDVAPEVGH KFCKDFPGFI
460 470 480 490 500
PSLLKRLLDE RQEIKRKMKA SKDPIEKKML DYRQRAIKIL ANSILPEEWV
510 520 530 540 550
PLIKNGKVKI FRIGDFVDGL MKANQGKVKK TGDTEVLEVA GIHAFSFDRK
560 570 580 590 600
SKKARVMAVK AVIRHRYSGN VYRIVLNSGR KITITEGHSL FVYRNGDLVE
610 620 630 640 650
ATGEDVKIGD LLAVPRSVNL PEKRERLNIV ELLLNLSPEE TEDIILTIPV
660 670 680 690 700
KGRKNFFKGM LRTLRWIFGE EKRVRTASRY LRHLENLGYI RLRKIGYDII
710 720 730 740 750
DKEGLEKYRT LYEKLVDVVR YNGNKREYLV EFNAVRDVIS LMPEEELKEW
760 770 780 790 800
RIGTRNGFRM GTFVDIDEDF AKLLGYYVSE GSARKWKNQT GGWSYTVRLY
810 820 830 840 850
NENDEVLDDM EHLAKKFFGK VKRGKNYVEI PKKMAYIIFE SLCGTLAENK
860 870 880 890 900
RVPEVIFTSS KGVRWAFLEG YFIGDGDVHP SKRVRLSTKS ELLVNGLVLL
910 920 930 940 950
LNSLGVSAIK LGYDSGVYRV YVNEELKFTE YRKKKNVYHS HIVPKDILKE
960 970 980 990 1000
TFGKVFQKNI SYKKFRELVE NGKLDREKAK RIEWLLNGDI VLDRVVEIKR
1010 1020 1030 1040 1050
EYYDGYVYDL SVDEDENFLA GFGFLYAHNS YYGYYGYAKA RWYCKECAES
1060 1070 1080 1090 1100
VTAWGREYIE FVRKELEEKF GFKVLYIDTD GLYATIPGAK PEEIKKKALE
1110 1120 1130 1140 1150
FVDYINAKLP GLLELEYEGF YVRGFFVTKK KYALIDEEGK IITRGLEIVR
1160 1170 1180 1190 1200
RDWSEIAKET QAKVLEAILK HGNVEEAVKI VKEVTEKLSK YEIPPEKLVI
1210 1220 1230 1240 1250
YEQITRPLHE YKAIGPHVAV AKRLAARGVK VRPGMVIGYI VLRGDGPISK
1260 1270 1280 1290 1300
RAILAEEFDL RKHKYDAEYY IENQVLPAVL RILEAFGYRK EDLRWQKTKQ
1310
TGLTAWLNIK KK
Length:1,312
Mass (Da):152,854
Last modified:November 1, 1996 - v1
Checksum:iB62518805641D26A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00707 Genomic DNA. Translation: AAA67130.1.
U00707 Genomic DNA. Translation: AAA67131.1.
U00707 Genomic DNA. Translation: AAA67132.1.
PIRiS68593.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00707 Genomic DNA. Translation: AAA67130.1.
U00707 Genomic DNA. Translation: AAA67131.1.
U00707 Genomic DNA. Translation: AAA67132.1.
PIRiS68593.

3D structure databases

ProteinModelPortaliQ51334.
SMRiQ51334. Positions 1-1310.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiN10.007.
REBASEi2619. PI-PspI.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

Gene3Di2.170.16.10. 2 hits.
3.10.28.10. 2 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.
IPR021133. HEAT_type_2.
IPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00136. DNA_pol_B. 2 hits.
PF03104. DNA_pol_B_exo1. 2 hits.
PF14528. LAGLIDADG_3. 1 hit.
[Graphical view]
PRINTSiPR00106. DNAPOLB.
PR00379. INTEIN.
SMARTiSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF51294. SSF51294. 2 hits.
SSF53098. SSF53098. 1 hit.
SSF55608. SSF55608. 1 hit.
TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
PS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "In vitro protein splicing of purified precursor and the identification of a branched intermediate."
    Xu M.-Q., Southworth M.W., Mersha F.B., Hornstra L.J., Perler F.B.
    Cell 75:1371-1377(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 493-517.

Entry informationi

Entry nameiDPOL_PYRSD
AccessioniPrimary (citable) accession number: Q51334
Secondary accession number(s): Q51335, Q51336
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: April 29, 2015
This is version 107 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

Direct protein sequencing

Documents

  1. Intein-containing proteins
    List of intein-containing protein entries
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.