DP2L_PYRAB
ID DP2L_PYRAB Reviewed; 1455 AA.
AC Q9V2F4; G8ZFV5;
DT 27-APR-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=DNA polymerase II large subunit;
DE Short=Pol II;
DE EC=2.7.7.7 {ECO:0000255|HAMAP-Rule:MF_00324};
DE AltName: Full=Exodeoxyribonuclease large subunit {ECO:0000255|HAMAP-Rule:MF_00324};
DE EC=3.1.11.1 {ECO:0000255|HAMAP-Rule:MF_00324};
DE Contains:
DE RecName: Full=Pab polC intein;
DE AltName: Full=Pab pol II intein;
GN Name=polC; OrderedLocusNames=PYRAB01200; ORFNames=PAB2404;
OS Pyrococcus abyssi (strain GE5 / Orsay).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=272844;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GE5 / Orsay;
RX PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x;
RA Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O.,
RA Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J.,
RA Weissenbach J., Zivanovic Y., Forterre P.;
RT "An integrated analysis of the genome of the hyperthermophilic archaeon
RT Pyrococcus abyssi.";
RL Mol. Microbiol. 47:1495-1512(2003).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=GE5 / Orsay;
RX PubMed=22057919; DOI=10.1007/s00284-011-0035-x;
RA Gao J., Wang J.;
RT "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and
RT Pyrococcus furiosus DSM 3638.";
RL Curr. Microbiol. 64:118-129(2012).
CC -!- FUNCTION: Possesses two activities: a DNA synthesis (polymerase) and an
CC exonucleolytic activity that degrades single-stranded DNA in the 3'- to
CC 5'-direction. Has a template-primer preference which is characteristic
CC of a replicative DNA polymerase (By similarity). {ECO:0000250}.
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 -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage in the 3'- to 5'-direction to yield
CC nucleoside 5'-phosphates.; EC=3.1.11.1; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00324};
CC -!- SUBUNIT: Heterodimer of a large subunit and a small subunit.
CC {ECO:0000250}.
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:0000305}.
CC -!- SIMILARITY: Belongs to the archaeal DNA polymerase II family.
CC {ECO:0000305}.
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DR EMBL; AJ248283; CAB49044.1; -; Genomic_DNA.
DR EMBL; HE613800; CCE69496.1; -; Genomic_DNA.
DR PIR; E75199; E75199.
DR RefSeq; WP_010867244.1; NC_000868.1.
DR PDB; 2LCJ; NMR; -; A=955-1139.
DR PDB; 5IJL; X-ray; 2.19 A; A=2-1246.
DR PDB; 6HMS; EM; 7.10 A; B=1-1455.
DR PDB; 6T7Y; X-ray; 2.70 A; B=1440-1451.
DR PDB; 6T8H; EM; 3.77 A; B=2-1455.
DR PDBsum; 2LCJ; -.
DR PDBsum; 5IJL; -.
DR PDBsum; 6HMS; -.
DR PDBsum; 6T7Y; -.
DR PDBsum; 6T8H; -.
DR AlphaFoldDB; Q9V2F4; -.
DR BMRB; Q9V2F4; -.
DR SMR; Q9V2F4; -.
DR STRING; 272844.PAB2404; -.
DR MEROPS; N10.005; -.
DR EnsemblBacteria; CAB49044; CAB49044; PAB2404.
DR GeneID; 1495007; -.
DR KEGG; pab:PAB2404; -.
DR PATRIC; fig|272844.11.peg.133; -.
DR eggNOG; arCOG04447; Archaea.
DR HOGENOM; CLU_001154_0_0_2; -.
DR OMA; KRRNCDG; -.
DR OrthoDB; 559at2157; -.
DR PhylomeDB; Q9V2F4; -.
DR BRENDA; 2.7.7.7; 5242.
DR Proteomes; UP000000810; Chromosome.
DR Proteomes; UP000009139; Chromosome.
DR GO; GO:0008408; F:3'-5' exonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008852; F:exodeoxyribonuclease I activity; IEA:UniProtKB-EC.
DR GO; GO:0000738; P:DNA catabolic process, exonucleolytic; IEA:UniProtKB-UniRule.
DR GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule.
DR GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR HAMAP; MF_00324; DNApol_II_L_arch; 1.
DR InterPro; IPR003587; Hint_dom_N.
DR InterPro; IPR036844; Hint_dom_sf.
DR InterPro; IPR030934; Intein_C.
DR InterPro; IPR006141; Intein_N.
DR InterPro; IPR004475; PolC_DP2.
DR InterPro; IPR016033; PolC_DP2_N.
DR PANTHER; PTHR42210; PTHR42210; 1.
DR Pfam; PF03833; PolC_DP2; 1.
DR SMART; SM00306; HintN; 1.
DR SUPFAM; SSF51294; SSF51294; 1.
DR TIGRFAMs; TIGR01445; intein_Nterm; 1.
DR TIGRFAMs; TIGR00354; polC; 1.
DR PROSITE; PS50818; INTEIN_C_TER; 1.
DR PROSITE; PS50817; INTEIN_N_TER; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Autocatalytic cleavage; DNA replication; DNA-binding;
KW DNA-directed DNA polymerase; Exonuclease; Hydrolase;
KW Multifunctional enzyme; Nuclease; Nucleotidyltransferase; Protein splicing;
KW Transferase.
FT CHAIN 1..954
FT /note="DNA polymerase II large subunit, 1st part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000007304"
FT CHAIN 955..1139
FT /note="Pab polC intein"
FT /evidence="ECO:0000255"
FT /id="PRO_0000007305"
FT CHAIN 1140..1455
FT /note="DNA polymerase II large subunit, 2nd part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000007306"
FT REGION 1409..1440
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1418..1440
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT HELIX 5..29
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 43..46
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 47..55
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 60..71
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 73..85
FT /evidence="ECO:0007829|PDB:5IJL"
FT TURN 86..89
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 95..110
FT /evidence="ECO:0007829|PDB:5IJL"
FT TURN 111..113
FT /evidence="ECO:0007829|PDB:5IJL"
FT TURN 117..121
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 122..129
FT /evidence="ECO:0007829|PDB:5IJL"
FT TURN 131..134
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 137..143
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 145..150
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 151..168
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 178..194
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 204..213
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 215..219
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 224..227
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 239..241
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 243..251
FT /evidence="ECO:0007829|PDB:5IJL"
FT TURN 252..256
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 257..267
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 273..283
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 312..322
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 344..346
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 349..355
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 369..374
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 400..402
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 406..409
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 414..416
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 420..426
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 427..429
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 430..435
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 438..443
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 460..475
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 487..497
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 501..509
FT /evidence="ECO:0007829|PDB:5IJL"
FT TURN 511..513
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 518..528
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 534..536
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 540..542
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 545..558
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 560..566
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 569..578
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 579..582
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 585..591
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 596..599
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 602..606
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 609..614
FT /evidence="ECO:0007829|PDB:5IJL"
FT TURN 615..617
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 618..620
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 632..639
FT /evidence="ECO:0007829|PDB:5IJL"
FT TURN 678..681
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 682..684
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 687..692
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 697..701
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 707..709
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 712..714
FT /evidence="ECO:0007829|PDB:5IJL"
FT TURN 719..721
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 726..730
FT /evidence="ECO:0007829|PDB:5IJL"
FT TURN 732..734
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 737..739
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 740..745
FT /evidence="ECO:0007829|PDB:5IJL"
FT TURN 746..748
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 753..756
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 761..765
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 767..778
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 789..791
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 794..796
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 802..811
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 823..829
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 831..833
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 835..838
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 842..847
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 872..876
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 877..896
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 909..912
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 916..920
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 926..943
FT /evidence="ECO:0007829|PDB:5IJL"
FT TURN 945..948
FT /evidence="ECO:0007829|PDB:5IJL"
FT TURN 950..955
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 960..966
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 969..974
FT /evidence="ECO:0007829|PDB:2LCJ"
FT HELIX 975..978
FT /evidence="ECO:0007829|PDB:2LCJ"
FT HELIX 979..981
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 985..988
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 991..994
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 996..999
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 1001..1007
FT /evidence="ECO:0007829|PDB:2LCJ"
FT TURN 1008..1011
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 1012..1025
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 1030..1035
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 1040..1043
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 1045..1053
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 1056..1061
FT /evidence="ECO:0007829|PDB:2LCJ"
FT HELIX 1062..1064
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 1070..1073
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 1083..1086
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 1103..1111
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 1114..1119
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 1126..1131
FT /evidence="ECO:0007829|PDB:2LCJ"
FT TURN 1132..1134
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 1135..1138
FT /evidence="ECO:0007829|PDB:2LCJ"
FT STRAND 1144..1149
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 1150..1156
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 1159..1161
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 1162..1165
FT /evidence="ECO:0007829|PDB:5IJL"
FT STRAND 1174..1177
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 1200..1205
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 1206..1208
FT /evidence="ECO:0007829|PDB:5IJL"
FT HELIX 1212..1222
FT /evidence="ECO:0007829|PDB:5IJL"
SQ SEQUENCE 1455 AA; 165711 MW; BB092E7BB2FE0D21 CRC64;
MELPKEMEEY FEMLQREIDK AYEIAKKARA QGKDPSLDVE IPQATDMAGR VESLVGPPGV
AKRIRELVKE YGKEIAALKI VDEIIEGKFG DLGSREKYAE QAVRTALAIL TEGIVSAPIE
GIANVKIKRN TWADNSEYLA LYYAGPIRSS GGTAQALSVL VGDYVRRKLG LDRFKPSEKH
IERMVEEVDL YHRAVTRLQY HPSPEEVRLA MRNIPIEITG EATDDVEVSH RDVPGVETNQ
LRGGAILVLA EGVLQKAKKL VKYIDKMGIE GWEWLKEFVE AKEKGEPKEE GKEESLAEST
LEETKVEVDM GFYYSLYQKF KEEIAPSDKY AKEVIGGRPL FSDPSKPGGF RLRYGRSRAS
GFATWGINPA TMILVDEFLA IGTQLKTERP GKGAVVTPVT TIEGPIVKLK DGSVLRVDDY
NLALKVREDV EEILYLGDAV IAFGDFVENN QTLLPANYCE EWWILEFVKA LKEIYEVHLE
PFTENEEESI EEASDYLEID PEFLKEMLRD PLRVKPPVEL AIHFSEVLGI PLHPYYTLYW
NSVEPKDVEK LWRLLKNYAE IEWSNFRGIK FAKKIVISQE KLGDSKRTLE LLGLPHTVRD
GNVIVDYPWA AALLTPLGNL NWEFMAKPLY ATIDIINENN EIKLRDRGIS WIGARMGRPE
KAKERKMKPP VQVLFPIGLA GGSSRDIKKA AEEGKVAEVE IAFFKCPKCG HVGPEHLCPN
CGTRKELLWV CPRCNAEYPE SQAEGYNYTC PKCNVKLRPY AKRKIRPSEL LNRAMENVKV
YGVDKLKGVM GMTSGWKMPE PLEKGLLRAK NDVYVFKDGT IRFDATDAPI THFRPREIGV
SVEKLRELGY THDFEGKPLV SEDQIVELKP QDIILSKEAG RYLLKVAKFV DDLLEKFYGL
PRFYNAEKME DLIGHLVIGL APHTSAGIVG RIIGFVDALV GYAHPYFHAA KRRNCFPGDT
RILVQIDGVP QKITLRELYE LFEDERYENM VYVRKKPKRE IKVYSIDLET GKVVLTDIED
VIKAPATDHL IRFELEDGRS FETTVDHPVL VYENGRFIEK RAFEVKEGDK VLVSELELVE
QSSSSQDNPK NENLGSPEHD QLLEIKNIKY VRANDDFVFS LNAKKYHNVI INENIVTHQC
DGDEDAVMLL LDALLNFSRY YLPEKRGGKM DAPLVITTRL DPREVDSEVH NMDIVRYYPL
EFYEATYELK SPKELVGVIE RVEDRLGKPE MYYGLKFTHD TDDIALGPKM SLYKQLGDME
EKVRRQLEVA KRIRAVDEHG VAEKILNSHL IPDLRGNLRS FTRQEFRCVK CNTKFRRPPL
NGKCPVCGGK IVLTVSKGAI EKYLGTAKML VTEYNVKNYT RQRICLTERD IDSLFENVFP
ETQLTLIVNP NDICQRLVMA RTGEVNKSGL LENLSNGSKK TEKAEKAEKP RKKSDEKPKK
KRVISLEEFF SRKSK
