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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: -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

Keywordsi

Molecular functionDNA-binding, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase
Biological processDNA replication, Intron homing

Enzyme and pathway databases

BioCyciTKOD69014:G1G2A-2-MONOMER
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

Proteomic databases

PRIDEiP77933

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 strandi2 – 10Combined sources9
Beta strandi13 – 22Combined sources10
Beta strandi25 – 31Combined sources7
Beta strandi37 – 44Combined sources8
Helixi45 – 47Combined sources3
Helixi48 – 51Combined sources4
Beta strandi55 – 58Combined sources4
Beta strandi61 – 64Combined sources4
Beta strandi67 – 75Combined sources9
Beta strandi78 – 86Combined sources9
Helixi92 – 102Combined sources11
Beta strandi106 – 111Combined sources6
Helixi116 – 123Combined sources8
Beta strandi137 – 144Combined sources8
Beta strandi157 – 164Combined sources8
Beta strandi167 – 174Combined sources8
Beta strandi181 – 183Combined sources3
Helixi187 – 201Combined sources15
Beta strandi204 – 210Combined sources7
Turni211 – 214Combined sources4
Helixi215 – 226Combined sources12
Beta strandi240 – 244Combined sources5
Beta strandi247 – 251Combined sources5
Beta strandi255 – 259Combined sources5
Helixi260 – 267Combined sources8
Helixi275 – 283Combined sources9
Helixi292 – 301Combined sources10
Helixi305 – 337Combined sources33
Helixi341 – 346Combined sources6
Helixi349 – 363Combined sources15
Helixi374 – 379Combined sources6
Beta strandi395 – 406Combined sources12
Helixi768 – 776Combined sources9
Turni780 – 782Combined sources3
Beta strandi791 – 793Combined sources3
Turni795 – 797Combined sources3
Beta strandi800 – 802Combined sources3
Helixi810 – 828Combined sources19
Helixi833 – 852Combined sources20
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 – 1429Combined sources26
Beta strandi1432 – 1437Combined sources6
Beta strandi1440 – 1444Combined sources5
Helixi1450 – 1467Combined sources18
Beta strandi1474 – 1487Combined sources14
Beta strandi1490 – 1494Combined sources5
Beta strandi1500 – 1505Combined sources6
Helixi1506 – 1508Combined sources3
Beta strandi1510 – 1512Combined sources3
Helixi1514 – 1528Combined sources15
Helixi1533 – 1547Combined sources15
Turni1548 – 1550Combined sources3
Helixi1554 – 1557Combined sources4
Beta strandi1559 – 1562Combined sources4
Helixi1567 – 1569Combined sources3
Helixi1575 – 1585Combined sources11
Beta strandi1595 – 1602Combined sources8
Helixi1608 – 1610Combined sources3
Beta strandi1611 – 1613Combined sources3
Helixi1614 – 1616Combined sources3
Turni1619 – 1621Combined sources3
Helixi1626 – 1631Combined sources6
Helixi1634 – 1642Combined sources9
Helixi1643 – 1645Combined sources3
Helixi1649 – 1652Combined sources4

3D structure databases

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

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiarCOG00328 Archaea
arCOG03145 Archaea
COG0417 LUCA
HOGENOMiHOG000222650
InParanoidiP77933
KOiK02319
OMAiYAHNSYY
OrthoDBiPOG093Z00EA

Family and domain databases

Gene3Di3.10.28.10, 2 hits
3.30.420.10, 1 hit
3.90.1600.10, 3 hits
InterProiView protein in InterPro
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_sf
IPR003586 Hint_dom_C
IPR003587 Hint_dom_N
IPR036844 Hint_dom_sf
IPR027434 Homing_endonucl
IPR006142 INTEIN
IPR030934 Intein_C
IPR004042 Intein_endonuc
IPR006141 Intein_N
IPR004860 LAGLIDADG_2
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf
PfamiView protein in Pfam
PF00136 DNA_pol_B, 2 hits
PF03104 DNA_pol_B_exo1, 2 hits
PF14528 LAGLIDADG_3, 2 hits
PRINTSiPR00379 INTEIN
SMARTiView protein in SMART
SM00305 HintC, 2 hits
SM00306 HintN, 2 hits
SM00486 POLBc, 1 hit
SUPFAMiSSF51294 SSF51294, 4 hits
SSF53098 SSF53098, 1 hit
SSF55608 SSF55608, 2 hits
TIGRFAMsiTIGR01443 intein_Cterm, 2 hits
TIGR01445 intein_Nterm, 1 hit
PROSITEiView protein in PROSITE
PS00116 DNA_POLYMERASE_B, 1 hit
PS50818 INTEIN_C_TER, 2 hits
PS50819 INTEIN_ENDONUCLEASE, 2 hits
PS50817 INTEIN_N_TER, 2 hits

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
PATRICifig|69014.16.peg.1

Similar proteinsi

Entry informationi

Entry nameiDPOL_THEKO
AccessioniPrimary (citable) accession number: P77933
Secondary accession number(s): Q5JEA7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: March 29, 2005
Last modified: May 23, 2018
This is version 158 of the entry and version 3 of the sequence. See 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

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