ID Q5JET1_THEKO Unreviewed; 735 AA. AC Q5JET1; DT 15-FEB-2005, integrated into UniProtKB/TrEMBL. DT 15-FEB-2005, sequence version 1. DT 03-MAY-2023, entry version 117. DE RecName: Full=DNA polymerase II small subunit {ECO:0000256|HAMAP-Rule:MF_00325}; DE Short=Pol II {ECO:0000256|HAMAP-Rule:MF_00325}; DE EC=2.7.7.7 {ECO:0000256|HAMAP-Rule:MF_00325}; DE AltName: Full=Exodeoxyribonuclease small subunit {ECO:0000256|HAMAP-Rule:MF_00325}; DE EC=3.1.11.1 {ECO:0000256|HAMAP-Rule:MF_00325}; GN Name=polB {ECO:0000256|HAMAP-Rule:MF_00325}; GN ORFNames=TK1902 {ECO:0000313|EMBL:BAD86091.1}; OS Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) OS (Pyrococcus kodakaraensis (strain KOD1)). OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; OC Thermococcus. OX NCBI_TaxID=69014 {ECO:0000313|EMBL:BAD86091.1, ECO:0000313|Proteomes:UP000000536}; RN [1] {ECO:0000313|EMBL:BAD86091.1, ECO:0000313|Proteomes:UP000000536} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1 RC {ECO:0000313|Proteomes:UP000000536}; RX PubMed=15710748; DOI=10.1101/gr.3003105; RA Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.; RT "Complete genome sequence of the hyperthermophilic archaeon Thermococcus RT kodakaraensis KOD1 and comparison with Pyrococcus genomes."; RL Genome Res. 15:352-363(2005). RN [2] {ECO:0007829|PDB:6KNB, ECO:0007829|PDB:6KNC} RP STRUCTURE BY ELECTRON MICROSCOPY (6.90 ANGSTROMS) OF 263-735. RX PubMed=33115459; DOI=10.1186/s12915-020-00889-y; RA Mayanagi K., Oki K., Miyazaki N., Ishino S., Yamagami T., Morikawa K., RA Iwasaki K., Kohda D., Shirai T., Ishino Y.; RT "Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome RT complex, revealed by cryo-electron microscopy."; RL BMC Biol. 18:152-152(2020). RN [3] {ECO:0007829|PDB:7E15} RP X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) OF 1-64. RX PubMed=34568951; DOI=10.1093/nar/gkab799; RA Oki K., Nagata M., Yamagami T., Numata T., Ishino S., Oyama T., Ishino Y.; RT "Family D DNA polymerase interacts with GINS to promote CMG-helicase in the RT archaeal replisome."; RL Nucleic Acids Res. 0:0-0(2021). 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. {ECO:0000256|ARBA:ARBA00024817, CC ECO:0000256|HAMAP-Rule:MF_00325}. 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 Evidence={ECO:0000256|ARBA:ARBA00000563, ECO:0000256|HAMAP- CC Rule:MF_00325}; 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 Evidence={ECO:0000256|ARBA:ARBA00024632, ECO:0000256|HAMAP- CC Rule:MF_00325}; CC -!- SUBUNIT: Heterodimer of a large subunit and a small subunit. CC {ECO:0000256|ARBA:ARBA00011315, ECO:0000256|HAMAP-Rule:MF_00325}. CC -!- SIMILARITY: Belongs to the DNA polymerase delta/II small subunit CC family. {ECO:0000256|ARBA:ARBA00006035, ECO:0000256|HAMAP- CC Rule:MF_00325}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AP006878; BAD86091.1; -; Genomic_DNA. DR PDB; 6KNB; EM; 6.90 A; A=263-735. DR PDB; 6KNC; EM; 9.30 A; A=259-735. DR PDB; 7E15; X-ray; 2.45 A; C/F=1-64. DR AlphaFoldDB; Q5JET1; -. DR SMR; Q5JET1; -. DR STRING; 69014.TK1902; -. DR EnsemblBacteria; BAD86091; BAD86091; TK1902. DR KEGG; tko:TK1902; -. DR PATRIC; fig|69014.16.peg.1860; -. DR eggNOG; arCOG04455; Archaea. DR HOGENOM; CLU_027850_1_0_2; -. DR InParanoid; Q5JET1; -. DR OMA; FIGPGNH; -. DR OrthoDB; 372039at2157; -. DR PhylomeDB; Q5JET1; -. DR Proteomes; UP000000536; Chromosome. DR GO; GO:0042575; C:DNA polymerase complex; IBA:GO_Central. 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:0008310; F:single-stranded DNA 3'-5' DNA exonuclease activity; IEA:UniProtKB-EC. DR GO; GO:0000738; P:DNA catabolic process, exonucleolytic; IEA:UniProtKB-UniRule. DR GO; GO:0006271; P:DNA strand elongation involved in DNA replication; IBA:GO_Central. DR CDD; cd07386; MPP_DNA_pol_II_small_archeal_C; 1. DR CDD; cd04490; PolII_SU_OBF; 1. DR Gene3D; 3.60.21.50; -; 1. DR Gene3D; 1.10.8.800; D-family DNA polymerase, DP1 subunit N-terminal domain; 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; DNA POLYMERASE DELTA SUBUNIT 2; 1. DR PANTHER; PTHR10416:SF0; DNA POLYMERASE DELTA SUBUNIT 2; 1. DR Pfam; PF04042; DNA_pol_E_B; 1. DR SUPFAM; SSF56300; Metallo-dependent phosphatases; 1. DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1. PE 1: Evidence at protein level; KW 3D-structure {ECO:0007829|PDB:6KNB, ECO:0007829|PDB:6KNC}; KW DNA replication {ECO:0000256|ARBA:ARBA00022705, ECO:0000256|HAMAP- KW Rule:MF_00325}; KW DNA-binding {ECO:0000256|ARBA:ARBA00023125, ECO:0000256|HAMAP- KW Rule:MF_00325}; KW DNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00022932, KW ECO:0000256|HAMAP-Rule:MF_00325}; KW Exonuclease {ECO:0000256|HAMAP-Rule:MF_00325}; KW Hydrolase {ECO:0000256|HAMAP-Rule:MF_00325}; KW Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268, ECO:0000256|HAMAP- KW Rule:MF_00325}; Nuclease {ECO:0000256|HAMAP-Rule:MF_00325}; KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695, ECO:0000256|HAMAP- KW Rule:MF_00325}; Reference proteome {ECO:0000313|Proteomes:UP000000536}; KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP- KW Rule:MF_00325}. FT DOMAIN 469..672 FT /note="DNA polymerase alpha/delta/epsilon subunit B" FT /evidence="ECO:0000259|Pfam:PF04042" FT REGION 79..114 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 130..254 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 134..184 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 192..206 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 214..228 FT /note="Acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" SQ SEQUENCE 735 AA; 80784 MW; A84B94CBC2614C3B CRC64; MLVEDLLKNN YLITPSAYYL LSDHYKKAFT LAELIKFAKN RGTFVVDSNL AREFLAEKGI ISSGNGALDG SVLSGISVSE SPVKPNGEAV LESESDESGA IESSLQEGVE DGVESIAEPS AASVEDVVVA GESSLASEGS SLEDEINTEP ELSSSMDDGA EVVQSSEGDE TSISTGNALG SVDYGGSDSE SEALEEASSG GESFISTGTP EDEALLEESP EGEFPDENGF SDESLPVENG SENGYGDSEE YYENGDNGVK PKIVYGDYGV PIAYVADETP EEEKAYSTYS DLVIAPKEGF HYRAKEIPDE WELAFDVKNV KFEVPKVKNA QSKEGEVIIQ AYSSYFKSRL KKMRRIFREN PEIGTIVDIA KLSYVREDDV TIIGLVNEKR ETRKGYLFEI EDATGRIKVF IGSDKEGANE AYSTIMPDSV VAFRGTPGKG IFFANRVFLP DVPKFKRSKP PLEEKVYAIL LSDIHVGSNK FCEEAFIKFL EWLNGEVNSR TEEELVSRIK YIIIGGDVVD GVGIYPGQYN ELAIPDIFDQ YEALANLLKQ VPDHITMFIG PGNHDAARTA LPQPGFYEEY AKPLYKLKNA VIISNPAVIR LHGRDFLVAH GRGIEDVVDF VPNRSHHRPA EAMVELLKLR HIAPTFGNKV PIAPDPEDTL VIESVPDLFQ AGHVHVMQYK TYNGVFVINT GTWQAQTEFQ KMVNIIPTPA RVPIIDVETA RLRAVVRFDQ FCEGV //