DPOL_PYRSD
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 03-AUG-2022, entry version 133.
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; unclassified 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 Gene3D; 1.10.132.60; -; 1.
DR Gene3D; 3.10.28.10; -; 1.
DR Gene3D; 3.30.420.10; -; 1.
DR Gene3D; 3.90.1600.10; -; 2.
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 Pfam; PF00136; DNA_pol_B; 2.
DR Pfam; PF03104; DNA_pol_B_exo1; 2.
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; SSF51294; SSF51294; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF55608; SSF55608; 1.
DR SUPFAM; SSF56672; SSF56672; 2.
DR TIGRFAMs; TIGR01443; intein_Cterm; 1.
DR TIGRFAMs; TIGR01445; intein_Nterm; 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
