DP2S_PYRHO
ID DP2S_PYRHO Reviewed; 622 AA.
AC O57863;
DT 27-APR-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=DNA polymerase II small subunit;
DE Short=Pol II;
DE EC=2.7.7.7;
DE AltName: Full=Exodeoxyribonuclease small subunit;
DE EC=3.1.11.1;
GN Name=polB; OrderedLocusNames=PH0123;
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;
CC -!- SUBUNIT: Heterodimer of a large subunit and a small subunit.
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the DNA polymerase delta/II small subunit
CC family. {ECO:0000305}.
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DR EMBL; BA000001; BAA29192.1; -; Genomic_DNA.
DR PIR; A71233; A71233.
DR RefSeq; WP_010884237.1; NC_000961.1.
DR PDB; 2KXE; NMR; -; A=1-72.
DR PDBsum; 2KXE; -.
DR AlphaFoldDB; O57863; -.
DR BMRB; O57863; -.
DR SMR; O57863; -.
DR IntAct; O57863; 1.
DR MINT; O57863; -.
DR STRING; 70601.3256509; -.
DR EnsemblBacteria; BAA29192; BAA29192; BAA29192.
DR GeneID; 1444019; -.
DR KEGG; pho:PH0123; -.
DR eggNOG; arCOG04455; Archaea.
DR OMA; FIGPGNH; -.
DR OrthoDB; 11652at2157; -.
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:0000738; P:DNA catabolic process, exonucleolytic; IEA:UniProtKB-UniRule.
DR GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule.
DR Gene3D; 2.40.50.140; -; 1.
DR HAMAP; MF_00325; DNApol_II_A_arch; 1.
DR InterPro; IPR004843; Calcineurin-like_PHP_ApaH.
DR InterPro; IPR024826; DNA_pol_delta/II_ssu.
DR InterPro; IPR029052; Metallo-depent_PP-like.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR011149; Pol2_small_arc.
DR PANTHER; PTHR10416; PTHR10416; 1.
DR Pfam; PF00149; Metallophos; 1.
DR PIRSF; PIRSF000803; Arc_Pol2_small; 1.
DR SUPFAM; SSF56300; SSF56300; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA replication; DNA-binding; DNA-directed DNA polymerase;
KW Exonuclease; Hydrolase; Multifunctional enzyme; Nuclease;
KW Nucleotidyltransferase; Transferase.
FT CHAIN 1..622
FT /note="DNA polymerase II small subunit"
FT /id="PRO_0000096181"
FT REGION 76..113
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 97..113
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT HELIX 3..9
FT /evidence="ECO:0007829|PDB:2KXE"
FT TURN 10..12
FT /evidence="ECO:0007829|PDB:2KXE"
FT HELIX 17..28
FT /evidence="ECO:0007829|PDB:2KXE"
FT HELIX 34..44
FT /evidence="ECO:0007829|PDB:2KXE"
FT STRAND 47..49
FT /evidence="ECO:0007829|PDB:2KXE"
FT HELIX 51..61
FT /evidence="ECO:0007829|PDB:2KXE"
SQ SEQUENCE 622 AA; 70283 MW; 28C4D84D9163274D CRC64;
MDEFVKGLMK NGYLITPSAY YLLVGHFNEG KFSLIELIKF AKSRETFIID DEIANEFLKS
IGAEVELPQE IKEGYISTGE GSQKVPDHEE LEKITNESSV ESSISTGETP KTEELQPTLD
ILEEEIGDIE GGESSISTGD EVPEVENNNG GTVVVFDKYG YPFTYVPEEI EEELEEYPKY
EDVTIEINPN LEVVPIEKDY EIKFDVRRVK LKPPKVKSGS GKEGEIIVEA YASLFRSRLR
KLRRILRENP EVSNVIDIKK LKYVKGDEEV TIIGLVNSKK ETSKGLIFEV EDQTDRVKVF
LPKDSEDYRE ALKVLPDAVV AFKGVYSKRG IFFANRFYLP DVPLYRKQKP PLEEKVYAVL
TSDIHVGSKE FCEKAFIKFL EWLNGYVESK EEEEIVSRIR YLIIAGDVVD GIGIYPGQYS
DLIIPDIFDQ YEALANLLSN VPKHITIFIG PGNHDAARPA IPQPEFYEEY AKPLYKLKNT
VIISNPAVIR LHGRDFLIAH GRGIEDVVSF VPGLTHHKPG LPMVELLKMR HLAPTFGGKV
PIAPDPEDLL VIEEVPDLVQ MGHVHVYDTA VYRGVQLVNS ATWQAQTEFQ KMVNIVPTPG
LVPIVDVESA RVIKVLDFSR WC
