DP2S_PYRAB
ID DP2S_PYRAB Reviewed; 619 AA.
AC Q9V2F3; G8ZFV6;
DT 27-APR-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 124.
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=PYRAB01210; ORFNames=PAB2266;
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;
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; AJ248283; CAB49045.1; -; Genomic_DNA.
DR EMBL; HE613800; CCE69497.1; -; Genomic_DNA.
DR PIR; F75199; F75199.
DR RefSeq; WP_010867245.1; NC_000868.1.
DR PDB; 5IHE; X-ray; 2.50 A; A/B=145-619.
DR PDB; 6HMF; X-ray; 2.60 A; A/B=145-619.
DR PDB; 6HMS; EM; 7.10 A; A=225-619.
DR PDB; 6T8H; EM; 3.77 A; A=1-619.
DR PDBsum; 5IHE; -.
DR PDBsum; 6HMF; -.
DR PDBsum; 6HMS; -.
DR PDBsum; 6T8H; -.
DR AlphaFoldDB; Q9V2F3; -.
DR SMR; Q9V2F3; -.
DR STRING; 272844.PAB2266; -.
DR EnsemblBacteria; CAB49045; CAB49045; PAB2266.
DR GeneID; 1495008; -.
DR KEGG; pab:PAB2266; -.
DR PATRIC; fig|272844.11.peg.134; -.
DR eggNOG; arCOG04455; Archaea.
DR HOGENOM; CLU_027850_1_0_2; -.
DR OMA; FIGPGNH; -.
DR OrthoDB; 11652at2157; -.
DR PhylomeDB; Q9V2F3; -.
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 Gene3D; 2.40.50.140; -; 1.
DR HAMAP; MF_00325; DNApol_II_A_arch; 1.
DR InterPro; IPR007185; DNA_pol_a/d/e_bsu.
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; PF04042; DNA_pol_E_B; 1.
DR PIRSF; PIRSF000803; Arc_Pol2_small; 1.
DR SUPFAM; SSF50249; SSF50249; 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..619
FT /note="DNA polymerase II small subunit"
FT /id="PRO_0000096179"
FT REGION 78..122
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 78..92
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 93..108
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT STRAND 154..156
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 159..162
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 177..179
FT /evidence="ECO:0007829|PDB:6HMF"
FT STRAND 197..201
FT /evidence="ECO:0007829|PDB:5IHE"
FT HELIX 203..205
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 207..209
FT /evidence="ECO:0007829|PDB:5IHE"
FT HELIX 229..243
FT /evidence="ECO:0007829|PDB:5IHE"
FT HELIX 255..257
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 267..279
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 282..288
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 293..299
FT /evidence="ECO:0007829|PDB:5IHE"
FT HELIX 305..310
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 316..323
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 325..335
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 354..358
FT /evidence="ECO:0007829|PDB:5IHE"
FT HELIX 370..380
FT /evidence="ECO:0007829|PDB:5IHE"
FT HELIX 387..393
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 396..403
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 409..412
FT /evidence="ECO:0007829|PDB:5IHE"
FT HELIX 415..418
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 419..421
FT /evidence="ECO:0007829|PDB:5IHE"
FT HELIX 424..435
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 442..447
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 450..454
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 456..460
FT /evidence="ECO:0007829|PDB:5IHE"
FT HELIX 465..472
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 477..479
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 482..488
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 491..495
FT /evidence="ECO:0007829|PDB:5IHE"
FT HELIX 499..507
FT /evidence="ECO:0007829|PDB:5IHE"
FT HELIX 517..526
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 534..536
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 554..558
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 564..569
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 572..577
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 579..581
FT /evidence="ECO:0007829|PDB:5IHE"
FT HELIX 585..589
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 598..603
FT /evidence="ECO:0007829|PDB:5IHE"
FT TURN 604..607
FT /evidence="ECO:0007829|PDB:5IHE"
FT STRAND 608..614
FT /evidence="ECO:0007829|PDB:5IHE"
FT HELIX 616..618
FT /evidence="ECO:0007829|PDB:5IHE"
SQ SEQUENCE 619 AA; 69395 MW; F556800288784814 CRC64;
MDELVKALER AGYLLTPSAY YLLVDHFKEG KFSLVELVKF AKSKGVFIID GDLAYEFLQF
LGLGVPQEIK ESYISTGEEA EKTVESQETR ASELEEGGVS QVSSGELQEL KEESPEISTT
EEEIGGLELV QSSISTGSEV EYNNGENGES VVVLDKYGYP ILYAPEEIGE EKEYSKYEDV
VIEWNPSVTP VQIEKNYEVK FDVRQVKLRP PKVKNGSGKE GEIIVEAYAS LFKSRLSKLK
RILRENPEIS NVVDIGKLNY VSGDEEVTII GLVNSKRETN RGLIFEVEDK TGIVKVFLPK
DSEDYREAFK VLPDAVVAFK GFYSKKGIFF ANKFYLPDVP LYRKQKPPLE EKVYAILISD
IHVGSREFCE KAFLKFLEWL NGHVESKEEE EIVSRVKYLI IAGDVVDGIG IYPGQYSDLV
IPDIFDQYEA LANLLANVPE HITMFIGPGN HDAARPAIPQ PEFYKEYAKP IYKLKNAIII
SNPAVIRLHG RDFLIAHGRG IEDVVSFVPG LTHHKPGLPM VELLKMRHLA PTFGGKVPIA
PDPEDLLVIE EVPDLVQMGH VHVYDAVVYR GVQLVNSATW QAQTEFQKMV NIVPTPAKVP
VVDVESARVV KVLDFSGWC
