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DNA polymerase II large subunit (Pol II) (EC 2.7.7.7) [Cleaved into: Pab polC intein (Pab pol II intein)]

 DP2L_PYRAB              Reviewed;        1455 AA.
Q9V2F4; G8ZFV5;
27-APR-2001, integrated into UniProtKB/Swiss-Prot.
01-MAY-2000, sequence version 1.
25-OCT-2017, entry version 107.
RecName: Full=DNA polymerase II large subunit;
Short=Pol II;
EC=2.7.7.7;
Contains:
RecName: Full=Pab polC intein;
AltName: Full=Pab pol II intein;
Name=polC; OrderedLocusNames=PYRAB01200; ORFNames=PAB2404;
Pyrococcus abyssi (strain GE5 / Orsay).
Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
Pyrococcus.
NCBI_TaxID=272844;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=GE5 / Orsay;
PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x;
Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O.,
Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C.,
Van der Oost J., Weissenbach J., Zivanovic Y., Forterre P.;
"An integrated analysis of the genome of the hyperthermophilic
archaeon Pyrococcus abyssi.";
Mol. Microbiol. 47:1495-1512(2003).
[2]
GENOME REANNOTATION.
STRAIN=GE5 / Orsay;
PubMed=22057919; DOI=10.1007/s00284-011-0035-x;
Gao J., Wang J.;
"Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5
and Pyrococcus furiosus DSM 3638.";
Curr. Microbiol. 64:118-129(2012).
-!- FUNCTION: Possesses two activities: a DNA synthesis (polymerase)
and an exonucleolytic activity that degrades single-stranded DNA
in the 3'- to 5'-direction. Has a template-primer preference which
is characteristic of a replicative DNA polymerase (By similarity).
{ECO:0000250}.
-!- CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) =
diphosphate + DNA(n+1).
-!- CATALYTIC ACTIVITY: Degradation of single-stranded DNA. It acts
progressively in a 3'- to 5'-direction, releasing nucleoside 5'-
phosphates.
-!- SUBUNIT: Heterodimer of a large subunit and a small subunit.
{ECO:0000250}.
-!- PTM: This protein undergoes a protein self splicing that involves
a post-translational excision of the intervening region (intein)
followed by peptide ligation. {ECO:0000305}.
-!- SIMILARITY: Belongs to the archaeal DNA polymerase II family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AJ248283; CAB49044.1; -; Genomic_DNA.
EMBL; HE613800; CCE69496.1; -; Genomic_DNA.
PIR; E75199; E75199.
RefSeq; WP_010867244.1; NC_000868.1.
PDB; 2LCJ; NMR; -; A=955-1139.
PDB; 5IJL; X-ray; 2.19 A; A=2-1246.
PDBsum; 2LCJ; -.
PDBsum; 5IJL; -.
ProteinModelPortal; Q9V2F4; -.
SMR; Q9V2F4; -.
STRING; 272844.PAB2404; -.
MEROPS; N10.005; -.
EnsemblBacteria; CAB49044; CAB49044; PAB2404.
GeneID; 1495007; -.
KEGG; pab:PAB2404; -.
PATRIC; fig|272844.11.peg.133; -.
eggNOG; arCOG04447; Archaea.
eggNOG; COG1933; LUCA.
HOGENOM; HOG000286435; -.
KO; K02322; -.
OMA; KRRNCDG; -.
OrthoDB; POG093Z06CT; -.
BRENDA; 2.7.7.7; 5242.
Proteomes; UP000000810; Chromosome.
Proteomes; UP000009139; Chromosome.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
HAMAP; MF_00324; DNApol_II_L_arch; 1.
InterPro; IPR003587; Hint_dom_N.
InterPro; IPR036844; Hint_dom_sf.
InterPro; IPR030934; Intein_C.
InterPro; IPR006141; Intein_N.
InterPro; IPR004475; PolC_DP2.
InterPro; IPR016033; PolC_DP2_N.
PANTHER; PTHR42210; PTHR42210; 1.
Pfam; PF03833; PolC_DP2; 1.
SMART; SM00306; HintN; 1.
SUPFAM; SSF51294; SSF51294; 1.
TIGRFAMs; TIGR01445; intein_Nterm; 1.
TIGRFAMs; TIGR00354; polC; 1.
PROSITE; PS50818; INTEIN_C_TER; 1.
PROSITE; PS50817; INTEIN_N_TER; 1.
1: Evidence at protein level;
3D-structure; Autocatalytic cleavage; Complete proteome;
DNA replication; DNA-binding; DNA-directed DNA polymerase;
Exonuclease; Hydrolase; Multifunctional enzyme; Nuclease;
Nucleotidyltransferase; Protein splicing; Transferase.
CHAIN 1 954 DNA polymerase II large subunit, 1st
part. {ECO:0000255}.
/FTId=PRO_0000007304.
CHAIN 955 1139 Pab polC intein. {ECO:0000255}.
/FTId=PRO_0000007305.
CHAIN 1140 1455 DNA polymerase II large subunit, 2nd
part. {ECO:0000255}.
/FTId=PRO_0000007306.
HELIX 5 29 {ECO:0000244|PDB:5IJL}.
STRAND 43 46 {ECO:0000244|PDB:5IJL}.
HELIX 47 55 {ECO:0000244|PDB:5IJL}.
HELIX 60 71 {ECO:0000244|PDB:5IJL}.
HELIX 73 85 {ECO:0000244|PDB:5IJL}.
TURN 86 89 {ECO:0000244|PDB:5IJL}.
HELIX 95 110 {ECO:0000244|PDB:5IJL}.
TURN 111 113 {ECO:0000244|PDB:5IJL}.
TURN 117 121 {ECO:0000244|PDB:5IJL}.
STRAND 122 129 {ECO:0000244|PDB:5IJL}.
TURN 131 134 {ECO:0000244|PDB:5IJL}.
STRAND 137 143 {ECO:0000244|PDB:5IJL}.
HELIX 145 150 {ECO:0000244|PDB:5IJL}.
HELIX 151 168 {ECO:0000244|PDB:5IJL}.
HELIX 178 194 {ECO:0000244|PDB:5IJL}.
HELIX 204 213 {ECO:0000244|PDB:5IJL}.
STRAND 215 219 {ECO:0000244|PDB:5IJL}.
STRAND 224 227 {ECO:0000244|PDB:5IJL}.
STRAND 239 241 {ECO:0000244|PDB:5IJL}.
HELIX 243 251 {ECO:0000244|PDB:5IJL}.
TURN 252 256 {ECO:0000244|PDB:5IJL}.
HELIX 257 267 {ECO:0000244|PDB:5IJL}.
HELIX 273 283 {ECO:0000244|PDB:5IJL}.
HELIX 312 322 {ECO:0000244|PDB:5IJL}.
STRAND 344 346 {ECO:0000244|PDB:5IJL}.
STRAND 349 355 {ECO:0000244|PDB:5IJL}.
HELIX 369 374 {ECO:0000244|PDB:5IJL}.
STRAND 400 402 {ECO:0000244|PDB:5IJL}.
STRAND 406 409 {ECO:0000244|PDB:5IJL}.
STRAND 414 416 {ECO:0000244|PDB:5IJL}.
HELIX 420 426 {ECO:0000244|PDB:5IJL}.
HELIX 427 429 {ECO:0000244|PDB:5IJL}.
STRAND 430 435 {ECO:0000244|PDB:5IJL}.
STRAND 438 443 {ECO:0000244|PDB:5IJL}.
HELIX 460 475 {ECO:0000244|PDB:5IJL}.
HELIX 487 497 {ECO:0000244|PDB:5IJL}.
HELIX 501 509 {ECO:0000244|PDB:5IJL}.
TURN 511 513 {ECO:0000244|PDB:5IJL}.
HELIX 518 528 {ECO:0000244|PDB:5IJL}.
HELIX 534 536 {ECO:0000244|PDB:5IJL}.
HELIX 540 542 {ECO:0000244|PDB:5IJL}.
HELIX 545 558 {ECO:0000244|PDB:5IJL}.
STRAND 560 566 {ECO:0000244|PDB:5IJL}.
STRAND 569 578 {ECO:0000244|PDB:5IJL}.
HELIX 579 582 {ECO:0000244|PDB:5IJL}.
HELIX 585 591 {ECO:0000244|PDB:5IJL}.
STRAND 596 599 {ECO:0000244|PDB:5IJL}.
STRAND 602 606 {ECO:0000244|PDB:5IJL}.
HELIX 609 614 {ECO:0000244|PDB:5IJL}.
TURN 615 617 {ECO:0000244|PDB:5IJL}.
HELIX 618 620 {ECO:0000244|PDB:5IJL}.
HELIX 632 639 {ECO:0000244|PDB:5IJL}.
TURN 678 681 {ECO:0000244|PDB:5IJL}.
HELIX 682 684 {ECO:0000244|PDB:5IJL}.
HELIX 687 692 {ECO:0000244|PDB:5IJL}.
STRAND 697 701 {ECO:0000244|PDB:5IJL}.
STRAND 707 709 {ECO:0000244|PDB:5IJL}.
STRAND 712 714 {ECO:0000244|PDB:5IJL}.
TURN 719 721 {ECO:0000244|PDB:5IJL}.
STRAND 726 730 {ECO:0000244|PDB:5IJL}.
TURN 732 734 {ECO:0000244|PDB:5IJL}.
STRAND 737 739 {ECO:0000244|PDB:5IJL}.
HELIX 740 745 {ECO:0000244|PDB:5IJL}.
TURN 746 748 {ECO:0000244|PDB:5IJL}.
STRAND 753 756 {ECO:0000244|PDB:5IJL}.
STRAND 761 765 {ECO:0000244|PDB:5IJL}.
HELIX 767 778 {ECO:0000244|PDB:5IJL}.
STRAND 789 791 {ECO:0000244|PDB:5IJL}.
STRAND 794 796 {ECO:0000244|PDB:5IJL}.
HELIX 802 811 {ECO:0000244|PDB:5IJL}.
STRAND 823 829 {ECO:0000244|PDB:5IJL}.
STRAND 831 833 {ECO:0000244|PDB:5IJL}.
HELIX 835 838 {ECO:0000244|PDB:5IJL}.
HELIX 842 847 {ECO:0000244|PDB:5IJL}.
STRAND 872 876 {ECO:0000244|PDB:5IJL}.
HELIX 877 896 {ECO:0000244|PDB:5IJL}.
HELIX 909 912 {ECO:0000244|PDB:5IJL}.
STRAND 916 920 {ECO:0000244|PDB:5IJL}.
STRAND 926 943 {ECO:0000244|PDB:5IJL}.
TURN 945 948 {ECO:0000244|PDB:5IJL}.
TURN 950 955 {ECO:0000244|PDB:5IJL}.
STRAND 960 966 {ECO:0000244|PDB:2LCJ}.
STRAND 969 974 {ECO:0000244|PDB:2LCJ}.
HELIX 975 978 {ECO:0000244|PDB:2LCJ}.
HELIX 979 981 {ECO:0000244|PDB:2LCJ}.
STRAND 985 988 {ECO:0000244|PDB:2LCJ}.
STRAND 991 994 {ECO:0000244|PDB:2LCJ}.
STRAND 996 999 {ECO:0000244|PDB:2LCJ}.
STRAND 1001 1007 {ECO:0000244|PDB:2LCJ}.
TURN 1008 1011 {ECO:0000244|PDB:2LCJ}.
STRAND 1012 1025 {ECO:0000244|PDB:2LCJ}.
STRAND 1030 1035 {ECO:0000244|PDB:2LCJ}.
STRAND 1040 1043 {ECO:0000244|PDB:2LCJ}.
STRAND 1045 1053 {ECO:0000244|PDB:2LCJ}.
STRAND 1056 1061 {ECO:0000244|PDB:2LCJ}.
HELIX 1062 1064 {ECO:0000244|PDB:2LCJ}.
STRAND 1070 1073 {ECO:0000244|PDB:2LCJ}.
STRAND 1083 1086 {ECO:0000244|PDB:2LCJ}.
STRAND 1103 1111 {ECO:0000244|PDB:2LCJ}.
STRAND 1114 1119 {ECO:0000244|PDB:2LCJ}.
STRAND 1126 1131 {ECO:0000244|PDB:2LCJ}.
TURN 1132 1134 {ECO:0000244|PDB:2LCJ}.
STRAND 1135 1138 {ECO:0000244|PDB:2LCJ}.
STRAND 1144 1149 {ECO:0000244|PDB:5IJL}.
HELIX 1150 1156 {ECO:0000244|PDB:5IJL}.
HELIX 1159 1161 {ECO:0000244|PDB:5IJL}.
STRAND 1162 1165 {ECO:0000244|PDB:5IJL}.
STRAND 1174 1177 {ECO:0000244|PDB:5IJL}.
HELIX 1200 1205 {ECO:0000244|PDB:5IJL}.
HELIX 1206 1208 {ECO:0000244|PDB:5IJL}.
HELIX 1212 1222 {ECO:0000244|PDB:5IJL}.
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


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