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P77933

- DPOL_THEKO

UniProt

P77933 - DPOL_THEKO

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Protein

DNA polymerase

Gene
pol, TK0001
Organism
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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 activityi

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

Temperature dependencei

Thermostable.

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

Enzyme and pathway databases

BioCyciTKOD69014:GH72-1-MONOMER.

Protein family/group databases

MEROPSiN10.007.
REBASEi3792. PI-PkoI.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase (EC:2.7.7.7)
Cleaved into the following 2 chains:
Alternative name(s):
IVS-A
Pko pol-1 intein
Alternative name(s):
IVS-B
Pko pol-2 intein
Gene namesi
Name:pol
Ordered Locus Names:TK0001
OrganismiThermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Taxonomic identifieri69014 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
ProteomesiUP000000536: Chromosome

Pathology & Biotechi

Biotechnological usei

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 406406DNA polymerase, 1st partPRO_0000007325Add
BLAST
Chaini407 – 766360Endonuclease PI-PkoIPRO_0000007326Add
BLAST
Chaini767 – 85185DNA polymerase, 2nd partPRO_0000007327Add
BLAST
Chaini852 – 1388537Endonuclease PI-PkoIIPRO_0000007328Add
BLAST
Chaini1389 – 1671283DNA polymerase, 3rd partPRO_0000007329Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi788 ↔ 802
Disulfide bondi1403 ↔ 1406

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 Reviewed prediction.

Keywords - PTMi

Autocatalytic cleavage, Disulfide bond, Protein splicing

Interactioni

Protein-protein interaction databases

STRINGi69014.TK0001.

Structurei

Secondary structure

1
1671
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 105
Beta strandi13 – 208
Beta strandi23 – 253
Beta strandi27 – 315
Beta strandi37 – 437
Turni45 – 473
Helixi48 – 514
Beta strandi56 – 583
Beta strandi61 – 633
Beta strandi68 – 758
Beta strandi78 – 869
Helixi90 – 956
Helixi97 – 1026
Beta strandi106 – 1116
Helixi116 – 1238
Beta strandi137 – 1448
Beta strandi157 – 1626
Turni164 – 1663
Beta strandi169 – 1746
Beta strandi181 – 1833
Helixi187 – 20115
Beta strandi204 – 2107
Turni211 – 2144
Helixi215 – 22410
Turni225 – 2273
Beta strandi241 – 2444
Beta strandi247 – 2504
Beta strandi255 – 2595
Helixi260 – 2678
Helixi275 – 2839
Helixi292 – 3009
Helixi305 – 33733
Helixi341 – 3444
Helixi349 – 36315
Helixi374 – 3807
Beta strandi395 – 40511
Helixi768 – 7769
Turni780 – 7823
Beta strandi791 – 7933
Turni795 – 7973
Beta strandi800 – 8023
Helixi808 – 82821
Helixi833 – 85018
Beta strandi858 – 8636
Beta strandi866 – 8716
Helixi872 – 88110
Helixi884 – 8863
Beta strandi888 – 8903
Beta strandi893 – 8975
Beta strandi900 – 9067
Turni908 – 9103
Beta strandi913 – 93523
Beta strandi940 – 9445
Beta strandi948 – 9536
Beta strandi956 – 9616
Turni962 – 9643
Beta strandi970 – 9756
Beta strandi985 – 9873
Helixi988 – 9936
Helixi997 – 9993
Beta strandi1004 – 10118
Helixi1015 – 102612
Helixi1036 – 104611
Beta strandi1048 – 10514
Beta strandi1053 – 10597
Helixi1061 – 107717
Beta strandi1079 – 10813
Turni1082 – 10843
Beta strandi1085 – 10884
Helixi1091 – 10944
Helixi1095 – 10984
Helixi1103 – 11064
Beta strandi1110 – 11123
Beta strandi1118 – 11247
Helixi1127 – 113913
Beta strandi1140 – 11456
Turni1147 – 11504
Beta strandi1153 – 11597
Helixi1163 – 117715
Beta strandi1184 – 11896
Helixi1192 – 120211
Helixi1206 – 12083
Helixi1213 – 12153
Helixi1220 – 123415
Beta strandi1240 – 12489
Helixi1250 – 126213
Beta strandi1268 – 12725
Beta strandi1277 – 12815
Turni1292 – 12954
Helixi1298 – 13003
Helixi1304 – 13118
Helixi1321 – 13299
Helixi1335 – 13384
Helixi1339 – 13413
Helixi1342 – 13465
Beta strandi1347 – 137125
Turni1372 – 13743
Beta strandi1376 – 13794
Beta strandi1384 – 13874
Helixi1390 – 13945
Helixi1404 – 142623
Turni1427 – 14293
Beta strandi1435 – 14373
Beta strandi1440 – 14434
Helixi1450 – 146718
Beta strandi1478 – 14858
Beta strandi1491 – 14944
Helixi1517 – 152711
Turni1528 – 15303
Helixi1534 – 15418
Turni1542 – 15509
Helixi1555 – 15573
Turni1577 – 15826
Beta strandi1614 – 16174
Beta strandi1620 – 16223
Helixi1630 – 16345
Helixi1635 – 16417
Helixi1649 – 16535

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WN7X-ray2.75A1-810[»]
1WNSX-ray3.00A1-1671[»]
2CW7X-ray2.70A852-1388[»]
2CW8X-ray2.50A852-1388[»]
ProteinModelPortaliP77933.
SMRiP77933. Positions 1-406, 763-1669.

Miscellaneous databases

EvolutionaryTraceiP77933.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini524 – 665142DOD-type homing endonuclease 1Add
BLAST
Domaini1132 – 1265134DOD-type homing endonuclease 2Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni135 – 3261923'-5' exonucleaseAdd
BLAST

Sequence similaritiesi

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG0417.
HOGENOMiHOG000222650.
KOiK02319.

Family and domain databases

Gene3Di2.170.16.10. 3 hits.
3.10.28.10. 3 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.
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. 3 hits.
PF03104. DNA_pol_B_exo1. 2 hits.
PF14528. LAGLIDADG_3. 2 hits.
[Graphical view]
PRINTSiPR00379. INTEIN.
SMARTiSM00305. HintC. 2 hits.
SM00306. HintN. 2 hits.
SM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF51294. SSF51294. 4 hits.
SSF53098. SSF53098. 1 hit.
SSF55608. SSF55608. 2 hits.
TIGRFAMsiTIGR01443. intein_Cterm. 2 hits.
TIGR01445. intein_Nterm. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
PS50818. INTEIN_C_TER. 2 hits.
PS50819. INTEIN_ENDONUCLEASE. 2 hits.
PS50817. INTEIN_N_TER. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P77933-1 [UniParc]FASTAAdd to Basket

« Hide

MILDTDYITE DGKPVIRIFK KENGEFKIEY DRTFEPYFYA LLKDDSAIEE     50
VKKITAERHG TVVTVKRVEK VQKKFLGRPV EVWKLYFTHP QDVPAIRDKI 100
REHPAVIDIY EYDIPFAKRY LIDKGLVPME GDEELKMLAF DIETLYHEGE 150
EFAEGPILMI SYADEEGARV ITWKNVDLPY VDVVSTEREM IKRFLRVVKE 200
KDPDVLITYN GDNFDFAYLK KRCEKLGINF ALGRDGSEPK IQRMGDRFAV 250
EVKGRIHFDL YPVIRRTINL PTYTLEAVYE AVFGQPKEKV YAEEITTAWE 300
TGENLERVAR YSMEDAKVTY ELGKEFLPME AQLSRLIGQS LWDVSRSSTG 350
NLVEWFLLRK AYERNELAPN KPDEKELARR RQSYEGGYVK EPERGLWENI 400
VYLDFRCHPA DTKVVVKGKG IINISEVQEG DYVLGIDGWQ RVRKVWEYDY 450
KGELVNINGL KCTPNHKLPV VTKNERQTRI RDSLAKSFLT KKVKGKIITT 500
PLFYEIGRAT SENIPEEEVL KGELAGILLA EGTLLRKDVE YFDSSRKKRR 550
ISHQYRVEIT IGKDEEEFRD RITYIFERLF GITPSISEKK GTNAVTLKVA 600
KKNVYLKVKE IMDNIESLHA PSVLRGFFEG DGSVNRVRRS IVATQGTKNE 650
WKIKLVSKLL SQLGIPHQTY TYQYQENGKD RSRYILEITG KDGLILFQTL 700
IGFISERKNA LLNKAISQRE MNNLENNGFY RLSEFNVSTE YYEGKVYDLT 750
LEGTPYYFAN GILTHNSLYP SIIITHNVSP DTLNREGCKE YDVAPQVGHR 800
FCKDFPGFIP SLLGDLLEER QKIKKKMKAT IDPIERKLLD YRQRAIKILA 850
NSILPEEWLP VLEEGEVHFV RIGELIDRMM EENAGKVKRE GETEVLEVSG 900
LEVPSFNRRT KKAELKRVKA LIRHDYSGKV YTIRLKSGRR IKITSGHSLF 950
SVRNGELVEV TGDELKPGDL VAVPRRLELP ERNHVLNLVE LLLGTPEEET 1000
LDIVMTIPVK GKKNFFKGML RTLRWIFGEE KRPRTARRYL RHLEDLGYVR 1050
LKKIGYEVLD WDSLKNYRRL YEALVENVRY NGNKREYLVE FNSIRDAVGI 1100
MPLKELKEWK IGTLNGFRMS PLIEVDESLA KLLGYYVSEG YARKQRNPKN 1150
GWSYSVKLYN EDPEVLDDME RLASRFFGKV RRGRNYVEIP KKIGYLLFEN 1200
MCGVLAENKR IPEFVFTSPK GVRLAFLEGY FIGDGDVHPN KRLRLSTKSE 1250
LLANQLVLLL NSVGVSAVKL GHDSGVYRVY INEELPFVKL DKKKNAYYSH 1300
VIPKEVLSEV FGKVFQKNVS PQTFRKMVED GRLDPEKAQR LSWLIEGDVV 1350
LDRVESVDVE DYDGYVYDLS VEDNENFLVG FGLVYAHNSY YGYYGYARAR 1400
WYCKECAESV TAWGREYITM TIKEIEEKYG FKVIYSDTDG FFATIPGADA 1450
ETVKKKAMEF LKYINAKLPG ALELEYEGFY KRGFFVTKKK YAVIDEEGKI 1500
TTRGLEIVRR DWSEIAKETQ ARVLEALLKD GDVEKAVRIV KEVTEKLSKY 1550
EVPPEKLVIH EQITRDLKDY KATGPHVAVA KRLAARGVKI RPGTVISYIV 1600
LKGSGRIGDR AIPFDEFDPT KHKYDAEYYI ENQVLPAVER ILRAFGYRKE 1650
DLRYQKTRQV GLSAWLKPKG T 1671
Length:1,671
Mass (Da):193,405
Last modified:March 29, 2005 - v3
Checksum:iD9C0029BE7EE2203
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti911 – 9111K → N in BAA06142. 1 Publication
Sequence conflicti1120 – 11212SP → RK in BAA06142. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D29671 Genomic DNA. Translation: BAA06142.2.
AP006878 Genomic DNA. Translation: BAD84190.1.
PIRiS71551.
RefSeqiYP_182414.1. NC_006624.1.

Genome annotation databases

EnsemblBacteriaiBAD84190; BAD84190; TK0001.
GeneIDi3233723.
KEGGitko:TK0001.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D29671 Genomic DNA. Translation: BAA06142.2 .
AP006878 Genomic DNA. Translation: BAD84190.1 .
PIRi S71551.
RefSeqi YP_182414.1. NC_006624.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1WN7 X-ray 2.75 A 1-810 [» ]
1WNS X-ray 3.00 A 1-1671 [» ]
2CW7 X-ray 2.70 A 852-1388 [» ]
2CW8 X-ray 2.50 A 852-1388 [» ]
ProteinModelPortali P77933.
SMRi P77933. Positions 1-406, 763-1669.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 69014.TK0001.

Protein family/group databases

MEROPSi N10.007.
REBASEi 3792. PI-PkoI.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD84190 ; BAD84190 ; TK0001 .
GeneIDi 3233723.
KEGGi tko:TK0001.

Phylogenomic databases

eggNOGi COG0417.
HOGENOMi HOG000222650.
KOi K02319.

Enzyme and pathway databases

BioCyci TKOD69014:GH72-1-MONOMER.

Miscellaneous databases

EvolutionaryTracei P77933.

Family and domain databases

Gene3Di 2.170.16.10. 3 hits.
3.10.28.10. 3 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.
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. 3 hits.
PF03104. DNA_pol_B_exo1. 2 hits.
PF14528. LAGLIDADG_3. 2 hits.
[Graphical view ]
PRINTSi PR00379. INTEIN.
SMARTi SM00305. HintC. 2 hits.
SM00306. HintN. 2 hits.
SM00486. POLBc. 1 hit.
[Graphical view ]
SUPFAMi SSF51294. SSF51294. 4 hits.
SSF53098. SSF53098. 1 hit.
SSF55608. SSF55608. 2 hits.
TIGRFAMsi TIGR01443. intein_Cterm. 2 hits.
TIGR01445. intein_Nterm. 1 hit.
PROSITEi PS00116. DNA_POLYMERASE_B. 1 hit.
PS50818. INTEIN_C_TER. 2 hits.
PS50819. INTEIN_ENDONUCLEASE. 2 hits.
PS50817. INTEIN_N_TER. 2 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.

Entry informationi

Entry nameiDPOL_THEKO
AccessioniPrimary (citable) accession number: P77933
Secondary accession number(s): Q5JEA7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: March 29, 2005
Last modified: September 3, 2014
This is version 131 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Intein-containing proteins
    List of intein-containing protein entries
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi