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P77933 (DPOL_PYRKO) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 121. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA polymerase
EC=2.7.7.7

Cleaved into the following 2 chains:

  1. Endonuclease PI-PkoI
    EC=3.1.-.-
    Alternative name(s):
    IVS-A
    Pko pol-1 intein
  2. Endonuclease PI-PkoII
    EC=3.1.-.-
    Alternative name(s):
    IVS-B
    Pko pol-2 intein
Gene names
Name:pol
Ordered Locus Names:TK0001
OrganismPyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Thermococcus kodakaraensis (strain KOD1)) [Reference proteome] [HAMAP]
Taxonomic identifier69014 [NCBI]
Taxonomic lineageArchaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus ›

Protein attributes

Sequence length1671 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. PI-PkoI recognizes 5'-GATTTAGATCCCTGTACC-3' and PI-PkoII recognizes 5'-CAGCTACTACGGTTAC-3'.

Catalytic activity

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

Post-translational modification

This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation Potential.

Biotechnological use

Pyrococcus kodakaraensis enzyme is the fastest thermostable DNA polymerase known today (130 nucleotides/s) and is used in high-performance PCR.

Sequence similarities

Belongs to the DNA polymerase type-B family.

Contains 2 DOD-type homing endonuclease domains.

Biophysicochemical properties

Temperature dependence:

Thermostable.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 406406DNA polymerase, 1st part
PRO_0000007325
Chain407 – 766360Endonuclease PI-PkoI
PRO_0000007326
Chain767 – 85185DNA polymerase, 2nd part
PRO_0000007327
Chain852 – 1388537Endonuclease PI-PkoII
PRO_0000007328
Chain1389 – 1671283DNA polymerase, 3rd part
PRO_0000007329

Regions

Domain524 – 665142DOD-type homing endonuclease 1
Domain1132 – 1265134DOD-type homing endonuclease 2
Region135 – 3261923'-5' exonuclease

Amino acid modifications

Disulfide bond788 ↔ 802
Disulfide bond1403 ↔ 1406

Experimental info

Sequence conflict9111K → N in BAA06142. Ref.1
Sequence conflict1120 – 11212SP → RK in BAA06142. Ref.1

Secondary structure

1 ......................................................................................................................................................................................................................... 1671
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P77933 [UniParc].

Last modified March 29, 2005. Version 3.
Checksum: D9C0029BE7EE2203

FASTA1,671193,405
        10         20         30         40         50         60 
MILDTDYITE DGKPVIRIFK KENGEFKIEY DRTFEPYFYA LLKDDSAIEE VKKITAERHG 

        70         80         90        100        110        120 
TVVTVKRVEK VQKKFLGRPV EVWKLYFTHP QDVPAIRDKI REHPAVIDIY EYDIPFAKRY 

       130        140        150        160        170        180 
LIDKGLVPME GDEELKMLAF DIETLYHEGE EFAEGPILMI SYADEEGARV ITWKNVDLPY 

       190        200        210        220        230        240 
VDVVSTEREM IKRFLRVVKE KDPDVLITYN GDNFDFAYLK KRCEKLGINF ALGRDGSEPK 

       250        260        270        280        290        300 
IQRMGDRFAV EVKGRIHFDL YPVIRRTINL PTYTLEAVYE AVFGQPKEKV YAEEITTAWE 

       310        320        330        340        350        360 
TGENLERVAR YSMEDAKVTY ELGKEFLPME AQLSRLIGQS LWDVSRSSTG NLVEWFLLRK 

       370        380        390        400        410        420 
AYERNELAPN KPDEKELARR RQSYEGGYVK EPERGLWENI VYLDFRCHPA DTKVVVKGKG 

       430        440        450        460        470        480 
IINISEVQEG DYVLGIDGWQ RVRKVWEYDY KGELVNINGL KCTPNHKLPV VTKNERQTRI 

       490        500        510        520        530        540 
RDSLAKSFLT KKVKGKIITT PLFYEIGRAT SENIPEEEVL KGELAGILLA EGTLLRKDVE 

       550        560        570        580        590        600 
YFDSSRKKRR ISHQYRVEIT IGKDEEEFRD RITYIFERLF GITPSISEKK GTNAVTLKVA 

       610        620        630        640        650        660 
KKNVYLKVKE IMDNIESLHA PSVLRGFFEG DGSVNRVRRS IVATQGTKNE WKIKLVSKLL 

       670        680        690        700        710        720 
SQLGIPHQTY TYQYQENGKD RSRYILEITG KDGLILFQTL IGFISERKNA LLNKAISQRE 

       730        740        750        760        770        780 
MNNLENNGFY RLSEFNVSTE YYEGKVYDLT LEGTPYYFAN GILTHNSLYP SIIITHNVSP 

       790        800        810        820        830        840 
DTLNREGCKE YDVAPQVGHR FCKDFPGFIP SLLGDLLEER QKIKKKMKAT IDPIERKLLD 

       850        860        870        880        890        900 
YRQRAIKILA NSILPEEWLP VLEEGEVHFV RIGELIDRMM EENAGKVKRE GETEVLEVSG 

       910        920        930        940        950        960 
LEVPSFNRRT KKAELKRVKA LIRHDYSGKV YTIRLKSGRR IKITSGHSLF SVRNGELVEV 

       970        980        990       1000       1010       1020 
TGDELKPGDL VAVPRRLELP ERNHVLNLVE LLLGTPEEET LDIVMTIPVK GKKNFFKGML 

      1030       1040       1050       1060       1070       1080 
RTLRWIFGEE KRPRTARRYL RHLEDLGYVR LKKIGYEVLD WDSLKNYRRL YEALVENVRY 

      1090       1100       1110       1120       1130       1140 
NGNKREYLVE FNSIRDAVGI MPLKELKEWK IGTLNGFRMS PLIEVDESLA KLLGYYVSEG 

      1150       1160       1170       1180       1190       1200 
YARKQRNPKN GWSYSVKLYN EDPEVLDDME RLASRFFGKV RRGRNYVEIP KKIGYLLFEN 

      1210       1220       1230       1240       1250       1260 
MCGVLAENKR IPEFVFTSPK GVRLAFLEGY FIGDGDVHPN KRLRLSTKSE LLANQLVLLL 

      1270       1280       1290       1300       1310       1320 
NSVGVSAVKL GHDSGVYRVY INEELPFVKL DKKKNAYYSH VIPKEVLSEV FGKVFQKNVS 

      1330       1340       1350       1360       1370       1380 
PQTFRKMVED GRLDPEKAQR LSWLIEGDVV LDRVESVDVE DYDGYVYDLS VEDNENFLVG 

      1390       1400       1410       1420       1430       1440 
FGLVYAHNSY YGYYGYARAR WYCKECAESV TAWGREYITM TIKEIEEKYG FKVIYSDTDG 

      1450       1460       1470       1480       1490       1500 
FFATIPGADA ETVKKKAMEF LKYINAKLPG ALELEYEGFY KRGFFVTKKK YAVIDEEGKI 

      1510       1520       1530       1540       1550       1560 
TTRGLEIVRR DWSEIAKETQ ARVLEALLKD GDVEKAVRIV KEVTEKLSKY EVPPEKLVIH 

      1570       1580       1590       1600       1610       1620 
EQITRDLKDY KATGPHVAVA KRLAARGVKI RPGTVISYIV LKGSGRIGDR AIPFDEFDPT 

      1630       1640       1650       1660       1670 
KHKYDAEYYI ENQVLPAVER ILRAFGYRKE DLRYQKTRQV GLSAWLKPKG T

« Hide

References

« Hide 'large scale' references
[1]"Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR."
Takagi M., Nishioka M., Kakihara H., Kitabayashi M., Inoue H., Kawakami B., Oka M., Imanaka T.
Appl. Environ. Microbiol. 63:4504-4510(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[2]"Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes."
Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.
Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[3]"Characterization of two intein homing endonucleases encoded in the DNA polymerase gene of Pyrococcus kodakaraensis strain KOD1."
Nishioka M., Fujiwara S., Takagi M., Imanaka T.
Nucleic Acids Res. 26:4409-4412(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION OF INTEINS.
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[4]"Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1."
Hashimoto H., Nishioka M., Fujiwara S., Takagi M., Imanaka T., Inoue T., Kai Y.
J. Mol. Biol. 306:469-477(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF DNA POLYMERASE.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		D29671 Genomic DNA. Translation: BAA06142.2.
AP006878 Genomic DNA. Translation: BAD84190.1.
PIRS71551.
RefSeqYP_182414.1. NC_006624.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1WN7X-ray2.75A1-810[»]
1WNSX-ray3.00A1-1671[»]
2CW7X-ray2.70A852-1388[»]
2CW8X-ray2.50A852-1388[»]
ProteinModelPortalP77933.
SMRP77933. Positions 1-406, 763-1669.
ModBaseSearch...

Protein-protein interaction databases

STRING69014.TK0001.

Protein family/group databases

MEROPSN10.007.
REBASE3792. PI-PkoI.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAD84190; BAD84190; TK0001.
GeneID3233723.
KEGGtko:TK0001.

Phylogenomic databases

eggNOGCOG0417.
HOGENOMHOG000222650.
KOK02319.
OMANIYAHNS.
ProtClustDBCLSK2517665.

Family and domain databases

Gene3D3.90.1600.10. 2 hits.
InterProIPR006172. 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.
IPR004578. DNA-dir_DNA_pol_B_pol2.
IPR023211. DNA_pol_palm_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR006142. INTEIN.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamPF00136. DNA_pol_B. 3 hits.
PF03104. DNA_pol_B_exo1. 2 hits.
[Graphical view]
PRINTSPR00379. INTEIN.
SMARTSM00305. HintC. 2 hits.
SM00306. HintN. 2 hits.
SM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMSSF53098. RNaseH_fold. 1 hit.
TIGRFAMsTIGR01443. intein_Cterm. 2 hits.
TIGR01445. intein_Nterm. 1 hit.
TIGR00592. pol2. 2 hits.
PROSITEPS00116. DNA_POLYMERASE_B. 1 hit.
PS50818. INTEIN_C_TER. 2 hits.
PS50819. INTEIN_ENDONUCLEASE. 2 hits.
PS50817. INTEIN_N_TER. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP77933.

Entry information

Entry nameDPOL_PYRKO
AccessionPrimary (citable) accession number: P77933
Secondary accession number(s): Q5JEA7
Entry history
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: March 29, 2005
Last modified: May 1, 2013
This is version 121 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Intein-containing proteins

List of intein-containing protein entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents