Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

P77933

- DPOL_THEKO

UniProt

P77933 - DPOL_THEKO

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

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 – 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.
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:
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.
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: October 29, 2014
This is version 133 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