ID DPOL_PYRSD Reviewed; 1312 AA. AC Q51334; Q51335; Q51336; DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot. DT 01-NOV-1996, sequence version 1. DT 13-SEP-2023, entry version 136. DE RecName: Full=DNA polymerase; DE EC=2.7.7.7; DE AltName: Full=Deep vent DNA polymerase; DE Contains: DE RecName: Full=Homing endonuclease PI-PspI {ECO:0000303|PubMed:12654995, ECO:0000303|PubMed:8269515}; DE EC=3.1.-.- {ECO:0000269|PubMed:8269515}; DE AltName: Full=Psp-GDB pol intein; GN Name=pol; OS Pyrococcus sp. (strain GB-D). OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; OC Pyrococcus. OX NCBI_TaxID=69013; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 493-502, RP CHARACTERIZATION OF INTEIN ENDONUCLEASE ACTIVITY, BIOPHYSICOCHEMICAL RP PROPERTIES, PROTEIN SPLICING, AND DNA-BINDING. RC STRAIN=GB-D; RX PubMed=8269515; DOI=10.1016/0092-8674(93)90623-x; RA Xu M.-Q., Southworth M.W., Mersha F.B., Hornstra L.J., Perler F.B.; RT "In vitro protein splicing of purified precursor and the identification of RT a branched intermediate."; RL Cell 75:1371-1377(1993). RN [2] RP NOMENCLATURE. RX PubMed=12654995; DOI=10.1093/nar/gkg274; RA Roberts R.J., Belfort M., Bestor T., Bhagwat A.S., Bickle T.A., RA Bitinaite J., Blumenthal R.M., Degtyarev S.K., Dryden D.T., Dybvig K., RA Firman K., Gromova E.S., Gumport R.I., Halford S.E., Hattman S., RA Heitman J., Hornby D.P., Janulaitis A., Jeltsch A., Josephsen J., Kiss A., RA Klaenhammer T.R., Kobayashi I., Kong H., Krueger D.H., Lacks S., RA Marinus M.G., Miyahara M., Morgan R.D., Murray N.E., Nagaraja V., RA Piekarowicz A., Pingoud A., Raleigh E., Rao D.N., Reich N., Repin V.E., RA Selker E.U., Shaw P.C., Stein D.C., Stoddard B.L., Szybalski W., RA Trautner T.A., Van Etten J.L., Vitor J.M., Wilson G.G., Xu S.Y.; RT "A nomenclature for restriction enzymes, DNA methyltransferases, homing RT endonucleases and their genes."; RL Nucleic Acids Res. 31:1805-1812(2003). CC -!- FUNCTION: In addition to polymerase activity, this DNA polymerase CC exhibits 3' to 5' exonuclease activity. {ECO:0000250|UniProtKB:P77933}. CC -!- FUNCTION: Intein encoded endonucleases are thought to mediate intein CC mobility by site-specific recombination initiated by endonuclease CC cleavage at the 'homing site' in gene that lack the intein (Probable). CC Intein splicing has been shown to occur via a branched intermediate CC that is resolved as the reaction proceeds; formation of the branched CC intermediate is reversible in response to pH shifts (PubMed:8269515). CC {ECO:0000269|PubMed:8269515, ECO:0000305}. CC -!- CATALYTIC ACTIVITY: CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339, CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560, CC ChEBI:CHEBI:173112; EC=2.7.7.7; CC -!- BIOPHYSICOCHEMICAL PROPERTIES: CC pH dependence: CC Optimum pH for intein splicing is 4.5-6.5. CC {ECO:0000269|PubMed:8269515}; CC -!- PTM: This protein undergoes a protein self splicing that involves a CC post-translational excision of the intervening region (intein) followed CC by peptide ligation. {ECO:0000269|PubMed:8269515}. CC -!- BIOTECHNOLOGY: Used in the PCR method because of its high CC thermostability and low error rate. Sold by New England Biolabs. CC -!- SIMILARITY: Belongs to the DNA polymerase type-B family. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; U00707; AAA67130.1; -; Genomic_DNA. DR EMBL; U00707; AAA67131.1; -; Genomic_DNA. DR EMBL; U00707; AAA67132.1; -; Genomic_DNA. DR PIR; S68593; S68593. DR PDB; 5H12; X-ray; 2.50 A; A=1-1312. DR PDBsum; 5H12; -. DR AlphaFoldDB; Q51334; -. DR SMR; Q51334; -. DR REBASE; 2619; PI-PspI. DR BRENDA; 2.7.7.7; 17906. DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW. DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW. DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW. DR GO; GO:0000166; F:nucleotide binding; IEA:InterPro. DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW. DR GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro. DR GO; GO:0006314; P:intron homing; IEA:UniProtKB-KW. DR CDD; cd05780; DNA_polB_Kod1_like_exo; 1. DR CDD; cd00081; Hint; 2. DR Gene3D; 1.10.132.60; DNA polymerase family B, C-terminal domain; 1. DR Gene3D; 3.30.342.10; DNA Polymerase, chain B, domain 1; 1. DR Gene3D; 2.170.16.10; Hedgehog/Intein (Hint) domain; 1. DR Gene3D; 1.10.287.690; Helix hairpin bin; 2. DR Gene3D; 3.10.28.10; Homing endonucleases; 1. DR Gene3D; 1.10.8.1330; Intein homing endonuclease, domain III; 1. DR Gene3D; 1.10.10.1010; Intein homing endonuclease, domain IV; 1. DR Gene3D; 3.90.1600.10; Palm domain of DNA polymerase; 2. DR Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 1. DR InterPro; IPR006172; DNA-dir_DNA_pol_B. DR InterPro; IPR017964; DNA-dir_DNA_pol_B_CS. DR InterPro; IPR006133; DNA-dir_DNA_pol_B_exonuc. DR InterPro; IPR006134; DNA-dir_DNA_pol_B_multi_dom. DR InterPro; IPR043502; DNA/RNA_pol_sf. DR InterPro; IPR042087; DNA_pol_B_thumb. DR InterPro; IPR023211; DNA_pol_palm_dom_sf. DR InterPro; IPR021133; HEAT_type_2. DR InterPro; IPR003586; Hint_dom_C. DR InterPro; IPR003587; Hint_dom_N. DR InterPro; IPR036844; Hint_dom_sf. DR InterPro; IPR027434; Homing_endonucl. DR InterPro; IPR006142; INTEIN. DR InterPro; IPR030934; Intein_C. DR InterPro; IPR004042; Intein_endonuc. DR InterPro; IPR006141; Intein_N. DR InterPro; IPR004860; LAGLIDADG_2. DR InterPro; IPR041005; PI-TkoII_IV. DR InterPro; IPR012337; RNaseH-like_sf. DR InterPro; IPR036397; RNaseH_sf. DR NCBIfam; TIGR01443; intein_Cterm; 1. DR NCBIfam; TIGR01445; intein_Nterm; 1. DR NCBIfam; TIGR00592; pol2; 2. DR PANTHER; PTHR10322; DNA POLYMERASE CATALYTIC SUBUNIT; 1. DR PANTHER; PTHR10322:SF23; DNA POLYMERASE DELTA CATALYTIC SUBUNIT; 1. DR Pfam; PF00136; DNA_pol_B; 2. DR Pfam; PF03104; DNA_pol_B_exo1; 2. DR Pfam; PF14890; Intein_splicing; 1. DR Pfam; PF14528; LAGLIDADG_3; 1. DR Pfam; PF18714; PI-TkoII_IV; 1. DR PRINTS; PR00106; DNAPOLB. DR PRINTS; PR00379; INTEIN. DR SMART; SM00305; HintC; 1. DR SMART; SM00306; HintN; 1. DR SMART; SM00486; POLBc; 1. DR SUPFAM; SSF56672; DNA/RNA polymerases; 2. DR SUPFAM; SSF51294; Hedgehog/intein (Hint) domain; 1. DR SUPFAM; SSF55608; Homing endonucleases; 1. DR SUPFAM; SSF53098; Ribonuclease H-like; 1. DR PROSITE; PS00116; DNA_POLYMERASE_B; 1. DR PROSITE; PS50818; INTEIN_C_TER; 1. DR PROSITE; PS50819; INTEIN_ENDONUCLEASE; 1. DR PROSITE; PS50817; INTEIN_N_TER; 1. PE 1: Evidence at protein level; KW 3D-structure; Autocatalytic cleavage; Direct protein sequencing; KW DNA replication; DNA-binding; DNA-directed DNA polymerase; Endonuclease; KW Hydrolase; Intron homing; Nuclease; Nucleotidyltransferase; KW Protein splicing; Transferase. FT CHAIN 1..492 FT /note="DNA polymerase, 1st part" FT /id="PRO_0000007330" FT CHAIN 493..1029 FT /note="Homing endonuclease PI-PspI" FT /evidence="ECO:0000269|PubMed:8269515" FT /id="PRO_0000007331" FT CHAIN 1030..1312 FT /note="DNA polymerase, 2nd part" FT /id="PRO_0000007332" FT DOMAIN 773..906 FT /note="DOD-type homing endonuclease" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00273" FT STRAND 2..10 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 13..21 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 26..31 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 37..43 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 45..47 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 48..51 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 55..58 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 61..64 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 67..75 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 78..86 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 90..92 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 93..101 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 106..111 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 116..124 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 137..144 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 157..163 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 168..174 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 181..183 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 187..201 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 204..210 FT /evidence="ECO:0007829|PDB:5H12" FT TURN 211..214 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 215..225 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 255..259 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 260..265 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 275..283 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 292..300 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 305..337 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 341..344 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 349..363 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 374..381 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 396..408 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 409..416 FT /evidence="ECO:0007829|PDB:5H12" FT TURN 421..423 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 432..434 FT /evidence="ECO:0007829|PDB:5H12" FT TURN 436..438 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 441..443 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 449..469 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 474..491 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 1031..1035 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 1045..1068 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 1073..1078 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 1081..1085 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 1091..1108 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 1115..1128 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 1131..1135 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 1141..1145 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 1155..1169 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 1174..1189 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 1195..1198 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 1208..1210 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 1216..1226 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 1239..1243 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 1248..1251 FT /evidence="ECO:0007829|PDB:5H12" FT STRAND 1252..1254 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 1255..1257 FT /evidence="ECO:0007829|PDB:5H12" FT TURN 1260..1262 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 1267..1272 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 1275..1284 FT /evidence="ECO:0007829|PDB:5H12" FT TURN 1285..1287 FT /evidence="ECO:0007829|PDB:5H12" FT HELIX 1290..1293 FT /evidence="ECO:0007829|PDB:5H12" SQ SEQUENCE 1312 AA; 152854 MW; B62518805641D26A CRC64; MILDADYITE DGKPIIRIFK KENGEFKVEY DRNFRPYIYA LLKDDSQIDE VRKITAERHG KIVRIIDAEK VRKKFLGRPI EVWRLYFEHP QDVPAIRDKI REHSAVIDIF EYDIPFAKRY LIDKGLIPME GDEELKLLAF DIETLYHEGE EFAKGPIIMI SYADEEEAKV ITWKKIDLPY VEVVSSEREM IKRFLKVIRE KDPDVIITYN GDSFDLPYLV KRAEKLGIKL PLGRDGSEPK MQRLGDMTAV EIKGRIHFDL YHVIRRTINL PTYTLEAVYE AIFGKPKEKV YAHEIAEAWE TGKGLERVAK YSMEDAKVTY ELGREFFPME AQLSRLVGQP LWDVSRSSTG NLVEWYLLRK AYERNELAPN KPDEREYERR LRESYAGGYV KEPEKGLWEG LVSLDFRSLY PSIIITHNVS PDTLNREGCR EYDVAPEVGH KFCKDFPGFI PSLLKRLLDE RQEIKRKMKA SKDPIEKKML DYRQRAIKIL ANSILPEEWV PLIKNGKVKI FRIGDFVDGL MKANQGKVKK TGDTEVLEVA GIHAFSFDRK SKKARVMAVK AVIRHRYSGN VYRIVLNSGR KITITEGHSL FVYRNGDLVE ATGEDVKIGD LLAVPRSVNL PEKRERLNIV ELLLNLSPEE TEDIILTIPV KGRKNFFKGM LRTLRWIFGE EKRVRTASRY LRHLENLGYI RLRKIGYDII DKEGLEKYRT LYEKLVDVVR YNGNKREYLV EFNAVRDVIS LMPEEELKEW RIGTRNGFRM GTFVDIDEDF AKLLGYYVSE GSARKWKNQT GGWSYTVRLY NENDEVLDDM EHLAKKFFGK VKRGKNYVEI PKKMAYIIFE SLCGTLAENK RVPEVIFTSS KGVRWAFLEG YFIGDGDVHP SKRVRLSTKS ELLVNGLVLL LNSLGVSAIK LGYDSGVYRV YVNEELKFTE YRKKKNVYHS HIVPKDILKE TFGKVFQKNI SYKKFRELVE NGKLDREKAK RIEWLLNGDI VLDRVVEIKR EYYDGYVYDL SVDEDENFLA GFGFLYAHNS YYGYYGYAKA RWYCKECAES VTAWGREYIE FVRKELEEKF GFKVLYIDTD GLYATIPGAK PEEIKKKALE FVDYINAKLP GLLELEYEGF YVRGFFVTKK KYALIDEEGK IITRGLEIVR RDWSEIAKET QAKVLEAILK HGNVEEAVKI VKEVTEKLSK YEIPPEKLVI YEQITRPLHE YKAIGPHVAV AKRLAARGVK VRPGMVIGYI VLRGDGPISK RAILAEEFDL RKHKYDAEYY IENQVLPAVL RILEAFGYRK EDLRWQKTKQ TGLTAWLNIK KK //