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P77933

- DPOL_THEKO

UniProt

P77933 - DPOL_THEKO

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Protein

DNA polymerase

Gene

pol

Organism
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed - Annotation score: 4 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.Curated

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP77933.

Family & Domainsi

Domains and Repeats

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

Region

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

Sequence similaritiesi

Belongs to the DNA polymerase type-B family.Curated
Contains 2 DOD-type homing endonuclease domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG0417.
HOGENOMiHOG000222650.
InParanoidiP77933.
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

        10         20         30         40         50
MILDTDYITE DGKPVIRIFK KENGEFKIEY DRTFEPYFYA LLKDDSAIEE
60 70 80 90 100
VKKITAERHG TVVTVKRVEK VQKKFLGRPV EVWKLYFTHP QDVPAIRDKI
110 120 130 140 150
REHPAVIDIY EYDIPFAKRY LIDKGLVPME GDEELKMLAF DIETLYHEGE
160 170 180 190 200
EFAEGPILMI SYADEEGARV ITWKNVDLPY VDVVSTEREM IKRFLRVVKE
210 220 230 240 250
KDPDVLITYN GDNFDFAYLK KRCEKLGINF ALGRDGSEPK IQRMGDRFAV
260 270 280 290 300
EVKGRIHFDL YPVIRRTINL PTYTLEAVYE AVFGQPKEKV YAEEITTAWE
310 320 330 340 350
TGENLERVAR YSMEDAKVTY ELGKEFLPME AQLSRLIGQS LWDVSRSSTG
360 370 380 390 400
NLVEWFLLRK AYERNELAPN KPDEKELARR RQSYEGGYVK EPERGLWENI
410 420 430 440 450
VYLDFRCHPA DTKVVVKGKG IINISEVQEG DYVLGIDGWQ RVRKVWEYDY
460 470 480 490 500
KGELVNINGL KCTPNHKLPV VTKNERQTRI RDSLAKSFLT KKVKGKIITT
510 520 530 540 550
PLFYEIGRAT SENIPEEEVL KGELAGILLA EGTLLRKDVE YFDSSRKKRR
560 570 580 590 600
ISHQYRVEIT IGKDEEEFRD RITYIFERLF GITPSISEKK GTNAVTLKVA
610 620 630 640 650
KKNVYLKVKE IMDNIESLHA PSVLRGFFEG DGSVNRVRRS IVATQGTKNE
660 670 680 690 700
WKIKLVSKLL SQLGIPHQTY TYQYQENGKD RSRYILEITG KDGLILFQTL
710 720 730 740 750
IGFISERKNA LLNKAISQRE MNNLENNGFY RLSEFNVSTE YYEGKVYDLT
760 770 780 790 800
LEGTPYYFAN GILTHNSLYP SIIITHNVSP DTLNREGCKE YDVAPQVGHR
810 820 830 840 850
FCKDFPGFIP SLLGDLLEER QKIKKKMKAT IDPIERKLLD YRQRAIKILA
860 870 880 890 900
NSILPEEWLP VLEEGEVHFV RIGELIDRMM EENAGKVKRE GETEVLEVSG
910 920 930 940 950
LEVPSFNRRT KKAELKRVKA LIRHDYSGKV YTIRLKSGRR IKITSGHSLF
960 970 980 990 1000
SVRNGELVEV TGDELKPGDL VAVPRRLELP ERNHVLNLVE LLLGTPEEET
1010 1020 1030 1040 1050
LDIVMTIPVK GKKNFFKGML RTLRWIFGEE KRPRTARRYL RHLEDLGYVR
1060 1070 1080 1090 1100
LKKIGYEVLD WDSLKNYRRL YEALVENVRY NGNKREYLVE FNSIRDAVGI
1110 1120 1130 1140 1150
MPLKELKEWK IGTLNGFRMS PLIEVDESLA KLLGYYVSEG YARKQRNPKN
1160 1170 1180 1190 1200
GWSYSVKLYN EDPEVLDDME RLASRFFGKV RRGRNYVEIP KKIGYLLFEN
1210 1220 1230 1240 1250
MCGVLAENKR IPEFVFTSPK GVRLAFLEGY FIGDGDVHPN KRLRLSTKSE
1260 1270 1280 1290 1300
LLANQLVLLL NSVGVSAVKL GHDSGVYRVY INEELPFVKL DKKKNAYYSH
1310 1320 1330 1340 1350
VIPKEVLSEV FGKVFQKNVS PQTFRKMVED GRLDPEKAQR LSWLIEGDVV
1360 1370 1380 1390 1400
LDRVESVDVE DYDGYVYDLS VEDNENFLVG FGLVYAHNSY YGYYGYARAR
1410 1420 1430 1440 1450
WYCKECAESV TAWGREYITM TIKEIEEKYG FKVIYSDTDG FFATIPGADA
1460 1470 1480 1490 1500
ETVKKKAMEF LKYINAKLPG ALELEYEGFY KRGFFVTKKK YAVIDEEGKI
1510 1520 1530 1540 1550
TTRGLEIVRR DWSEIAKETQ ARVLEALLKD GDVEKAVRIV KEVTEKLSKY
1560 1570 1580 1590 1600
EVPPEKLVIH EQITRDLKDY KATGPHVAVA KRLAARGVKI RPGTVISYIV
1610 1620 1630 1640 1650
LKGSGRIGDR AIPFDEFDPT KHKYDAEYYI ENQVLPAVER ILRAFGYRKE
1660 1670
DLRYQKTRQV GLSAWLKPKG T
Length:1,671
Mass (Da):193,405
Last modified:March 29, 2005 - v3
Checksum:iD9C0029BE7EE2203
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti911 – 9111K → N in BAA06142. (PubMed:9361436)Curated
Sequence conflicti1120 – 11212SP → RK in BAA06142. (PubMed:9361436)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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.
InParanoidi P77933.
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: November 26, 2014
This is version 134 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