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Protein

DNA polymerase

Gene

pol

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

GO - Biological processi

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

BRENDAi2.7.7.7. 5246.

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 kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Taxonomic identifieri69014 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
Proteomesi
  • UP000000536 Componenti: 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)DescriptionActionsGraphical viewLength
ChainiPRO_00000073251 – 406DNA polymerase, 1st partAdd BLAST406
ChainiPRO_0000007326407 – 766Endonuclease PI-PkoIAdd BLAST360
ChainiPRO_0000007327767 – 851DNA polymerase, 2nd partAdd BLAST85
ChainiPRO_0000007328852 – 1388Endonuclease PI-PkoIIAdd BLAST537
ChainiPRO_00000073291389 – 1671DNA polymerase, 3rd partAdd BLAST283

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi788 ↔ 802Combined sources1 Publication
Disulfide bondi1403 ↔ 1406Combined sources1 Publication

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

11671
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 10Combined sources5
Beta strandi13 – 20Combined sources8
Beta strandi23 – 25Combined sources3
Beta strandi27 – 31Combined sources5
Beta strandi37 – 43Combined sources7
Turni45 – 47Combined sources3
Helixi48 – 51Combined sources4
Beta strandi56 – 58Combined sources3
Beta strandi61 – 63Combined sources3
Beta strandi68 – 75Combined sources8
Beta strandi78 – 86Combined sources9
Helixi90 – 95Combined sources6
Helixi97 – 102Combined sources6
Beta strandi106 – 111Combined sources6
Helixi116 – 123Combined sources8
Beta strandi137 – 144Combined sources8
Beta strandi157 – 162Combined sources6
Turni164 – 166Combined sources3
Beta strandi169 – 174Combined sources6
Beta strandi181 – 183Combined sources3
Helixi187 – 201Combined sources15
Beta strandi204 – 210Combined sources7
Turni211 – 214Combined sources4
Helixi215 – 224Combined sources10
Turni225 – 227Combined sources3
Beta strandi241 – 244Combined sources4
Beta strandi247 – 250Combined sources4
Beta strandi255 – 259Combined sources5
Helixi260 – 267Combined sources8
Helixi275 – 283Combined sources9
Helixi292 – 300Combined sources9
Helixi305 – 337Combined sources33
Helixi341 – 344Combined sources4
Helixi349 – 363Combined sources15
Helixi374 – 380Combined sources7
Beta strandi395 – 405Combined sources11
Helixi768 – 776Combined sources9
Turni780 – 782Combined sources3
Beta strandi791 – 793Combined sources3
Turni795 – 797Combined sources3
Beta strandi800 – 802Combined sources3
Helixi808 – 828Combined sources21
Helixi833 – 850Combined sources18
Beta strandi858 – 863Combined sources6
Beta strandi866 – 871Combined sources6
Helixi872 – 881Combined sources10
Helixi884 – 886Combined sources3
Beta strandi888 – 890Combined sources3
Beta strandi893 – 897Combined sources5
Beta strandi900 – 906Combined sources7
Turni908 – 910Combined sources3
Beta strandi913 – 935Combined sources23
Beta strandi940 – 944Combined sources5
Beta strandi948 – 953Combined sources6
Beta strandi956 – 961Combined sources6
Turni962 – 964Combined sources3
Beta strandi970 – 975Combined sources6
Beta strandi985 – 987Combined sources3
Helixi988 – 993Combined sources6
Helixi997 – 999Combined sources3
Beta strandi1004 – 1011Combined sources8
Helixi1015 – 1026Combined sources12
Helixi1036 – 1046Combined sources11
Beta strandi1048 – 1051Combined sources4
Beta strandi1053 – 1059Combined sources7
Helixi1061 – 1077Combined sources17
Beta strandi1079 – 1081Combined sources3
Turni1082 – 1084Combined sources3
Beta strandi1085 – 1088Combined sources4
Helixi1091 – 1094Combined sources4
Helixi1095 – 1098Combined sources4
Helixi1103 – 1106Combined sources4
Beta strandi1110 – 1112Combined sources3
Beta strandi1118 – 1124Combined sources7
Helixi1127 – 1139Combined sources13
Beta strandi1140 – 1145Combined sources6
Turni1147 – 1150Combined sources4
Beta strandi1153 – 1159Combined sources7
Helixi1163 – 1177Combined sources15
Beta strandi1184 – 1189Combined sources6
Helixi1192 – 1202Combined sources11
Helixi1206 – 1208Combined sources3
Helixi1213 – 1215Combined sources3
Helixi1220 – 1234Combined sources15
Beta strandi1240 – 1248Combined sources9
Helixi1250 – 1262Combined sources13
Beta strandi1268 – 1272Combined sources5
Beta strandi1277 – 1281Combined sources5
Turni1292 – 1295Combined sources4
Helixi1298 – 1300Combined sources3
Helixi1304 – 1311Combined sources8
Helixi1321 – 1329Combined sources9
Helixi1335 – 1338Combined sources4
Helixi1339 – 1341Combined sources3
Helixi1342 – 1346Combined sources5
Beta strandi1347 – 1371Combined sources25
Turni1372 – 1374Combined sources3
Beta strandi1376 – 1379Combined sources4
Beta strandi1384 – 1387Combined sources4
Helixi1390 – 1394Combined sources5
Helixi1404 – 1426Combined sources23
Turni1427 – 1429Combined sources3
Beta strandi1435 – 1437Combined sources3
Beta strandi1440 – 1443Combined sources4
Helixi1450 – 1467Combined sources18
Beta strandi1478 – 1485Combined sources8
Beta strandi1491 – 1494Combined sources4
Helixi1517 – 1527Combined sources11
Turni1528 – 1530Combined sources3
Helixi1534 – 1541Combined sources8
Turni1542 – 1550Combined sources9
Helixi1555 – 1557Combined sources3
Turni1577 – 1582Combined sources6
Beta strandi1614 – 1617Combined sources4
Beta strandi1620 – 1622Combined sources3
Helixi1630 – 1634Combined sources5
Helixi1635 – 1641Combined sources7
Helixi1649 – 1653Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WN7X-ray2.75A1-810[»]
1WNSX-ray3.00A1-1671[»]
2CW7X-ray2.70A852-1388[»]
2CW8X-ray2.50A852-1388[»]
ProteinModelPortaliP77933.
SMRiP77933.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP77933.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini524 – 665DOD-type homing endonuclease 1PROSITE-ProRule annotationAdd BLAST142
Domaini1132 – 1265DOD-type homing endonuclease 2PROSITE-ProRule annotationAdd BLAST134

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni135 – 3263'-5' exonucleaseCuratedAdd BLAST192

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

eggNOGiarCOG00328. Archaea.
arCOG03145. Archaea.
COG0417. LUCA.
HOGENOMiHOG000222650.
InParanoidiP77933.
KOiK02319.
OMAiLDCECCK.

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.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR004860. LAGLIDADG_2.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00136. DNA_pol_B. 2 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)DescriptionActionsGraphical viewLength
Sequence conflicti911K → N in BAA06142 (PubMed:9361436).Curated1
Sequence conflicti1120 – 1121SP → RK in BAA06142 (PubMed:9361436).Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D29671 Genomic DNA. Translation: BAA06142.2.
AP006878 Genomic DNA. Translation: BAD84190.1.
PIRiS71551.
RefSeqiWP_011248956.1. 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.
PIRiS71551.
RefSeqiWP_011248956.1. NC_006624.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WN7X-ray2.75A1-810[»]
1WNSX-ray3.00A1-1671[»]
2CW7X-ray2.70A852-1388[»]
2CW8X-ray2.50A852-1388[»]
ProteinModelPortaliP77933.
SMRiP77933.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi69014.TK0001.

Protein family/group databases

MEROPSiN10.007.
REBASEi3792. PI-PkoI.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiarCOG00328. Archaea.
arCOG03145. Archaea.
COG0417. LUCA.
HOGENOMiHOG000222650.
InParanoidiP77933.
KOiK02319.
OMAiLDCECCK.

Enzyme and pathway databases

BRENDAi2.7.7.7. 5246.

Miscellaneous databases

EvolutionaryTraceiP77933.

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.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR004860. LAGLIDADG_2.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00136. DNA_pol_B. 2 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]
ProtoNetiSearch...

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 2, 2016
This is version 146 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.