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Q51334

- DPOL_PYRSD

UniProt

Q51334 - DPOL_PYRSD

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Protein

DNA polymerase

Gene
pol
Organism
Pyrococcus sp. (strain GB-D)
Status
Reviewed - 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. intein-mediated protein splicing Source: InterPro
  2. 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

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.

Family & Domainsi

Domains and Repeats

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

Sequence similaritiesi

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.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
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

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MILDADYITE DGKPIIRIFK KENGEFKVEY DRNFRPYIYA LLKDDSQIDE     50
VRKITAERHG KIVRIIDAEK VRKKFLGRPI EVWRLYFEHP QDVPAIRDKI 100
REHSAVIDIF EYDIPFAKRY LIDKGLIPME GDEELKLLAF DIETLYHEGE 150
EFAKGPIIMI SYADEEEAKV ITWKKIDLPY VEVVSSEREM IKRFLKVIRE 200
KDPDVIITYN GDSFDLPYLV KRAEKLGIKL PLGRDGSEPK MQRLGDMTAV 250
EIKGRIHFDL YHVIRRTINL PTYTLEAVYE AIFGKPKEKV YAHEIAEAWE 300
TGKGLERVAK YSMEDAKVTY ELGREFFPME AQLSRLVGQP LWDVSRSSTG 350
NLVEWYLLRK AYERNELAPN KPDEREYERR LRESYAGGYV KEPEKGLWEG 400
LVSLDFRSLY PSIIITHNVS PDTLNREGCR EYDVAPEVGH KFCKDFPGFI 450
PSLLKRLLDE RQEIKRKMKA SKDPIEKKML DYRQRAIKIL ANSILPEEWV 500
PLIKNGKVKI FRIGDFVDGL MKANQGKVKK TGDTEVLEVA GIHAFSFDRK 550
SKKARVMAVK AVIRHRYSGN VYRIVLNSGR KITITEGHSL FVYRNGDLVE 600
ATGEDVKIGD LLAVPRSVNL PEKRERLNIV ELLLNLSPEE TEDIILTIPV 650
KGRKNFFKGM LRTLRWIFGE EKRVRTASRY LRHLENLGYI RLRKIGYDII 700
DKEGLEKYRT LYEKLVDVVR YNGNKREYLV EFNAVRDVIS LMPEEELKEW 750
RIGTRNGFRM GTFVDIDEDF AKLLGYYVSE GSARKWKNQT GGWSYTVRLY 800
NENDEVLDDM EHLAKKFFGK VKRGKNYVEI PKKMAYIIFE SLCGTLAENK 850
RVPEVIFTSS KGVRWAFLEG YFIGDGDVHP SKRVRLSTKS ELLVNGLVLL 900
LNSLGVSAIK LGYDSGVYRV YVNEELKFTE YRKKKNVYHS HIVPKDILKE 950
TFGKVFQKNI SYKKFRELVE NGKLDREKAK RIEWLLNGDI VLDRVVEIKR 1000
EYYDGYVYDL SVDEDENFLA GFGFLYAHNS YYGYYGYAKA RWYCKECAES 1050
VTAWGREYIE FVRKELEEKF GFKVLYIDTD GLYATIPGAK PEEIKKKALE 1100
FVDYINAKLP GLLELEYEGF YVRGFFVTKK KYALIDEEGK IITRGLEIVR 1150
RDWSEIAKET QAKVLEAILK HGNVEEAVKI VKEVTEKLSK YEIPPEKLVI 1200
YEQITRPLHE YKAIGPHVAV AKRLAARGVK VRPGMVIGYI VLRGDGPISK 1250
RAILAEEFDL RKHKYDAEYY IENQVLPAVL RILEAFGYRK EDLRWQKTKQ 1300
TGLTAWLNIK KK 1312
Length:1,312
Mass (Da):152,854
Last modified:November 1, 1996 - v1
Checksum:iB62518805641D26A
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
U00707 Genomic DNA. Translation: AAA67130.1 .
U00707 Genomic DNA. Translation: AAA67131.1 .
U00707 Genomic DNA. Translation: AAA67132.1 .
PIRi S68593.

3D structure databases

ProteinModelPortali Q51334.
SMRi Q51334. Positions 1-1310.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

REBASEi 2619. PI-PspI.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Family and domain databases

Gene3Di 2.170.16.10. 2 hits.
3.10.28.10. 2 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.
IPR021133. HEAT_type_2.
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. 2 hits.
PF03104. DNA_pol_B_exo1. 2 hits.
PF14528. LAGLIDADG_3. 1 hit.
[Graphical view ]
PRINTSi PR00106. DNAPOLB.
PR00379. INTEIN.
SMARTi SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00486. POLBc. 1 hit.
[Graphical view ]
SUPFAMi SSF51294. SSF51294. 2 hits.
SSF53098. SSF53098. 1 hit.
SSF55608. SSF55608. 1 hit.
TIGRFAMsi TIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEi PS00116. DNA_POLYMERASE_B. 1 hit.
PS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: September 3, 2014
This is version 103 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

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