DP2L_PYRHO
ID DP2L_PYRHO Reviewed; 1431 AA.
AC O57861;
DT 27-APR-2001, integrated into UniProtKB/Swiss-Prot.
DT 27-APR-2001, sequence version 2.
DT 03-AUG-2022, entry version 136.
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=Pho polC intein;
DE AltName: Full=Pho pol II intein;
GN Name=polC; OrderedLocusNames=PH0121;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
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 -!- INTERACTION:
CC O57861; O57861: polC; NbExp=3; IntAct=EBI-8553242, EBI-8553242;
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA29190.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; BA000001; BAA29190.1; ALT_INIT; Genomic_DNA.
DR PIR; G71232; G71232.
DR RefSeq; WP_048053037.1; NC_000961.1.
DR PDB; 3O59; X-ray; 2.20 A; X=1-297.
DR PDB; 5BKH; X-ray; 2.43 A; A=944-1123.
DR PDB; 7OEC; X-ray; 1.48 A; A=951-1117.
DR PDBsum; 3O59; -.
DR PDBsum; 5BKH; -.
DR PDBsum; 7OEC; -.
DR AlphaFoldDB; O57861; -.
DR SMR; O57861; -.
DR MINT; O57861; -.
DR STRING; 70601.3256507; -.
DR MEROPS; N10.005; -.
DR EnsemblBacteria; BAA29190; BAA29190; BAA29190.
DR GeneID; 1444018; -.
DR KEGG; pho:PH0121; -.
DR eggNOG; arCOG04447; Archaea.
DR OMA; KRRNCDG; -.
DR OrthoDB; 559at2157; -.
DR BRENDA; 2.7.7.7; 5244.
DR Proteomes; UP000000752; 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:0042802; F:identical protein binding; IPI:IntAct.
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 CDD; cd00085; HNHc; 1.
DR HAMAP; MF_00324; DNApol_II_L_arch; 1.
DR InterPro; IPR003586; Hint_dom_C.
DR InterPro; IPR003587; Hint_dom_N.
DR InterPro; IPR036844; Hint_dom_sf.
DR InterPro; IPR003615; HNH_nuc.
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; SM00305; HintC; 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..951
FT /note="DNA polymerase II large subunit, 1st part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000007307"
FT CHAIN 952..1117
FT /note="Pho polC intein"
FT /evidence="ECO:0000255"
FT /id="PRO_0000007308"
FT CHAIN 1118..1431
FT /note="DNA polymerase II large subunit, 2nd part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000007309"
FT REGION 1388..1431
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1396..1410
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1417..1431
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT HELIX 47..55
FT /evidence="ECO:0007829|PDB:3O59"
FT HELIX 60..71
FT /evidence="ECO:0007829|PDB:3O59"
FT HELIX 73..86
FT /evidence="ECO:0007829|PDB:3O59"
FT TURN 87..89
FT /evidence="ECO:0007829|PDB:3O59"
FT HELIX 95..110
FT /evidence="ECO:0007829|PDB:3O59"
FT TURN 111..113
FT /evidence="ECO:0007829|PDB:3O59"
FT HELIX 117..121
FT /evidence="ECO:0007829|PDB:3O59"
FT STRAND 122..129
FT /evidence="ECO:0007829|PDB:3O59"
FT TURN 131..134
FT /evidence="ECO:0007829|PDB:3O59"
FT STRAND 137..143
FT /evidence="ECO:0007829|PDB:3O59"
FT HELIX 145..149
FT /evidence="ECO:0007829|PDB:3O59"
FT HELIX 152..168
FT /evidence="ECO:0007829|PDB:3O59"
FT HELIX 178..194
FT /evidence="ECO:0007829|PDB:3O59"
FT HELIX 204..213
FT /evidence="ECO:0007829|PDB:3O59"
FT STRAND 215..220
FT /evidence="ECO:0007829|PDB:3O59"
FT HELIX 243..250
FT /evidence="ECO:0007829|PDB:3O59"
FT TURN 251..256
FT /evidence="ECO:0007829|PDB:3O59"
FT HELIX 257..267
FT /evidence="ECO:0007829|PDB:3O59"
FT HELIX 273..284
FT /evidence="ECO:0007829|PDB:3O59"
FT STRAND 958..963
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 966..971
FT /evidence="ECO:0007829|PDB:7OEC"
FT HELIX 972..977
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 983..985
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 988..991
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 993..996
FT /evidence="ECO:0007829|PDB:5BKH"
FT STRAND 998..1004
FT /evidence="ECO:0007829|PDB:7OEC"
FT TURN 1005..1008
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 1009..1013
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 1015..1022
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 1027..1032
FT /evidence="ECO:0007829|PDB:7OEC"
FT HELIX 1033..1035
FT /evidence="ECO:0007829|PDB:5BKH"
FT STRAND 1037..1041
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 1045..1050
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 1053..1058
FT /evidence="ECO:0007829|PDB:7OEC"
FT HELIX 1059..1061
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 1067..1071
FT /evidence="ECO:0007829|PDB:7OEC"
FT TURN 1073..1075
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 1078..1089
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 1093..1101
FT /evidence="ECO:0007829|PDB:7OEC"
FT TURN 1102..1104
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 1106..1109
FT /evidence="ECO:0007829|PDB:7OEC"
FT TURN 1110..1112
FT /evidence="ECO:0007829|PDB:7OEC"
FT STRAND 1113..1116
FT /evidence="ECO:0007829|PDB:7OEC"
SQ SEQUENCE 1431 AA; 162928 MW; 59B73A48868B6298 CRC64;
MELPKEMEEY FSMLQREIDK AYEIAKKARA QGKDPSLDVE IPQASDMAGR VESLVGPPGV
AERIRELVKE YGKEIAALKI VDEIIDGKFG DLGSKEKYAE QAVRTALAIL TEGVVSAPIE
GIASVKIKRN TWSDNSEYLA LYYAGPIRSS GGTAQALSVL VGDYVRRKLG LDRFKPSEKH
IERMVEEVDL YHRTVSRLQY HPSPEEVRLA MRNIPIEITG EATDEVEVSH RDIPGVETNQ
LRGGAILVLA EGVLQKAKKL VKYIDKMGIE GWEWLKEFVE AKEKGEEIEE EGSAESTVEE
TKVEVDMGFY YSLYQKFKSE IAPNDKYAKE IIGGRPLFSD PSRNGGFRLR YGRSRVSGFA
TWGINPATMI LVDEFLAIGT QLKTERPGKG AVVTPVTTIE GPIVKLKDGS VVKVDDYKLA
LKIRDEVEEI LYLGDAVIAF GDFVENNQTL LPANYCEEWW ILEFTKALNE IYEVELKPFE
VNSSEDLEEA ADYLEVDIEF LKELLKDPLR TKPPVELAIH FSEILGIPLH PYYTLYWNSV
KPEQVEKLWR VLKEHAHIDW DNFRGIKFAR RIVIPLEKLR DSKRALELLG LPHKVEGKNV
IVDYPWAAAL LTPLGNLEWE FRAKPLHTTI DIINENNEIK LRDRGISWIG ARMGRPEKAK
ERKMKPPVQV LFPIGLAGGS SRDIKKAAEE GKVAEVEIAL FKCPKCGHVG PEHICPNCGT
RKELIWVCPR CNAEYPESQA SGYNYTCPKC NVKLKPYAKR KIKPSELLKR AMDNVKVYGI
DKLKGVMGMT SGWKMPEPLE KGLLRAKNDV YVFKDGTIRF DATDAPITHF RPREIGVSVE
KLRELGYTHD FEGNPLVSED QIVELKPQDI ILSKEAGKYL LKVAKFVDDL LEKFYGLPRF
YNAEKMEDLI GHLVIGLAPH TSAGIVGRII GFVDALVGYA HPYFHAAKRR NCFPGDTRIL
VQINGTPQRV TLKELYELFD EEHYESMVYV RKKPKVDIKV YSFNPEEGKV VLTDIEEVIK
APATDHLIRF ELELGSSFET TVDHPVLVYE NGKFVEKRAF EVREGNIIII IDESTLEPLK
VAVKKIEFIE PPEDFVFSLN AKKYHTVIIN ENIVTHQCDG DEDAVMLLLD ALLNFSRYYL
PEKRGGKMDA PLVITTRLDP REVDSEVHNM DIVRYYPLEF YEATYELKSP KELVGVIERV
EDRLGKPEMY YGLKFTHDTD DIALGPKMSL YKQLGDMEEK VKRQLDVARR IRAVDEHKVA
ETILNSHLIP DLRGNLRSFT RQEFRCVKCN TKFRRPPLDG KCPICGGKIV LTVSKGAIEK
YLGTAKMLVT EYKVKNYTRQ RICLTERDID SLFETVFPET QLTLLVNPND ICQRIIMERT
GGSKKSGLLE NFANGYNKGK KEEMPKKQRK KEQEKSKKRK VISLDDFFSR K
