UniProtKB - P77933 (DPOL_THEKO)
DNA polymerase
pol
Functioni
Has high processivity, a high polymerization rate and high fidelity. In addition to polymerase activity, also exhibits 3' to 5' exonuclease activity.
1 PublicationIntein encoded endonucleases are thought to mediate intein mobility by site-specific recombination initiated by endonuclease cleavage at the 'homing site' in genes that lack the intein (Probable). Upon expression in E.coli PI-PkoI recognizes the minimal sequence 5'-GATTTTAGATCCCTGTACC-3' and cuts after T-10. PI-PkoII recognizes the minimal sequence 5'-CAGCTACTACGGTTAC-3' and cuts after C-10. Given the high intracellular K+ content (>0.5 M), PI-PkoII is probably more active than PI-PkoI in vivo (PubMed:9742242).
Curated1 PublicationCatalytic activityi
- EC:2.7.7.71 Publication
pH dependencei
Temperature dependencei
GO - Molecular functioni
- DNA binding Source: UniProtKB-KW
- DNA-directed DNA polymerase activity Source: GO_Central
- endonuclease activity Source: UniProtKB-KW
- nucleotide binding Source: InterPro
GO - Biological processi
- DNA-dependent DNA replication Source: GO_Central
- intein-mediated protein splicing Source: InterPro
- intron homing Source: UniProtKB-KW
Keywordsi
Molecular function | DNA-binding, DNA-directed DNA polymerase, Endonuclease, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase |
Biological process | DNA replication, Intron homing |
Enzyme and pathway databases
BRENDAi | 2.7.7.7, 5246 |
Protein family/group databases
MEROPSi | N10.007 |
REBASEi | 3792, PI-PkoI 3793, PI-PkoII |
Names & Taxonomyi
Protein namesi | Recommended name: DNA polymerase (EC:2.7.7.71 Publication)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 |
Organismi | Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1)) |
Taxonomic identifieri | 69014 [NCBI] |
Taxonomic lineagei | Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus › |
Proteomesi |
|
Pathology & Biotechi
Biotechnological usei
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000007325 | 1 – 407 | DNA polymerase, 1st partAdd BLAST | 407 | |
ChainiPRO_0000007326 | 408 – 766 | Homing endonuclease PI-PkoI1 PublicationAdd BLAST | 359 | |
ChainiPRO_0000007327 | 767 – 851 | DNA polymerase, 2nd partAdd BLAST | 85 | |
ChainiPRO_0000007328 | 852 – 1388 | Homing endonuclease PI-PkoII1 PublicationAdd BLAST | 537 | |
ChainiPRO_0000007329 | 1389 – 1671 | DNA polymerase, 3rd partAdd BLAST | 283 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Disulfide bondi | 788 ↔ 802 | Combined sources1 Publication | ||
Disulfide bondi | 1403 ↔ 1406 | Combined sources1 Publication |
Post-translational modificationi
Keywords - PTMi
Autocatalytic cleavage, Disulfide bond, Protein splicingStructurei
Secondary structure
3D structure databases
AlphaFoldDBi | P77933 |
SMRi | P77933 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P77933 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 524 – 665 | DOD-type homing endonuclease 1PROSITE-ProRule annotationAdd BLAST | 142 | |
Domaini | 1132 – 1265 | DOD-type homing endonuclease 2PROSITE-ProRule annotationAdd BLAST | 134 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 135 – 326 | 3'-5' exonucleaseCuratedAdd BLAST | 192 |
Sequence similaritiesi
Keywords - Domaini
RepeatPhylogenomic databases
eggNOGi | arCOG00328, Archaea arCOG03145, Archaea |
HOGENOMi | CLU_000203_6_4_2 |
InParanoidi | P77933 |
OMAi | YAHNSYY |
OrthoDBi | 35869at2157 |
Family and domain databases
Gene3Di | 1.10.132.60, 1 hit 3.10.28.10, 2 hits 3.30.420.10, 1 hit 3.90.1600.10, 3 hits |
InterProi | View 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 IPR043502, DNA/RNA_pol_sf IPR042087, DNA_pol_B_thumb 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 IPR041005, PI-TkoII_IV IPR012337, RNaseH-like_sf IPR036397, RNaseH_sf |
Pfami | View protein in Pfam PF00136, DNA_pol_B, 2 hits PF03104, DNA_pol_B_exo1, 2 hits PF14528, LAGLIDADG_3, 3 hits PF18714, PI-TkoII_IV, 1 hit |
PRINTSi | PR00379, INTEIN |
SMARTi | View protein in SMART SM00305, HintC, 2 hits SM00306, HintN, 2 hits SM00486, POLBc, 1 hit |
SUPFAMi | SSF51294, SSF51294, 2 hits SSF53098, SSF53098, 1 hit SSF55608, SSF55608, 2 hits SSF56672, SSF56672, 3 hits |
TIGRFAMsi | TIGR01443, intein_Cterm, 2 hits TIGR01445, intein_Nterm, 1 hit |
PROSITEi | View 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 |
i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
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
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 911 | K → N in BAA06142 (PubMed:9361436).Curated | 1 | |
Sequence conflicti | 1120 – 1121 | SP → RK in BAA06142 (PubMed:9361436).Curated | 2 |
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 | WP_011248956.1, NC_006624.1 |
Genome annotation databases
EnsemblBacteriai | BAD84190; BAD84190; TK0001 |
GeneIDi | 3233723 |
KEGGi | tko:TK0001 |
PATRICi | fig|69014.16.peg.1 |
Similar proteinsi
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 | WP_011248956.1, NC_006624.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB 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 | [»] | |
4K8Z | X-ray | 2.29 | A | 1-1671 | [»] | |
5OMF | X-ray | 2.09 | A | 1-1671 | [»] | |
6Q4T | X-ray | 2.00 | A | 1-1671 | [»] | |
7OM3 | X-ray | 1.92 | A | 1-1671 | [»] | |
7OMB | X-ray | 2.01 | A | 1-1671 | [»] | |
7OMG | X-ray | 2.10 | A | 1-1671 | [»] | |
AlphaFoldDBi | P77933 | |||||
SMRi | P77933 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
STRINGi | 69014.TK0001 |
Protein family/group databases
MEROPSi | N10.007 |
REBASEi | 3792, PI-PkoI 3793, PI-PkoII |
Genome annotation databases
EnsemblBacteriai | BAD84190; BAD84190; TK0001 |
GeneIDi | 3233723 |
KEGGi | tko:TK0001 |
PATRICi | fig|69014.16.peg.1 |
Phylogenomic databases
eggNOGi | arCOG00328, Archaea arCOG03145, Archaea |
HOGENOMi | CLU_000203_6_4_2 |
InParanoidi | P77933 |
OMAi | YAHNSYY |
OrthoDBi | 35869at2157 |
Enzyme and pathway databases
BRENDAi | 2.7.7.7, 5246 |
Miscellaneous databases
EvolutionaryTracei | P77933 |
Family and domain databases
Gene3Di | 1.10.132.60, 1 hit 3.10.28.10, 2 hits 3.30.420.10, 1 hit 3.90.1600.10, 3 hits |
InterProi | View 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 IPR043502, DNA/RNA_pol_sf IPR042087, DNA_pol_B_thumb 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 IPR041005, PI-TkoII_IV IPR012337, RNaseH-like_sf IPR036397, RNaseH_sf |
Pfami | View protein in Pfam PF00136, DNA_pol_B, 2 hits PF03104, DNA_pol_B_exo1, 2 hits PF14528, LAGLIDADG_3, 3 hits PF18714, PI-TkoII_IV, 1 hit |
PRINTSi | PR00379, INTEIN |
SMARTi | View protein in SMART SM00305, HintC, 2 hits SM00306, HintN, 2 hits SM00486, POLBc, 1 hit |
SUPFAMi | SSF51294, SSF51294, 2 hits SSF53098, SSF53098, 1 hit SSF55608, SSF55608, 2 hits SSF56672, SSF56672, 3 hits |
TIGRFAMsi | TIGR01443, intein_Cterm, 2 hits TIGR01445, intein_Nterm, 1 hit |
PROSITEi | View 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 |
MobiDBi | Search... |
Entry informationi
Entry namei | DPOL_THEKO | |
Accessioni | P77933Primary (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: | May 25, 2022 | |
This is version 175 of the entry and version 3 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- Intein-containing proteins
List of intein-containing protein entries - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families