POLK_CAEEL
ID POLK_CAEEL Reviewed; 596 AA.
AC P34409; A8WFE8; A8WFE9;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 25-JAN-2012, sequence version 3.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=DNA polymerase kappa;
DE EC=2.7.7.7;
GN Name=polk-1; ORFNames=F22B7.6;
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2;
RX PubMed=7906398; DOI=10.1038/368032a0;
RA Wilson R., Ainscough R., Anderson K., Baynes C., Berks M., Bonfield J.,
RA Burton J., Connell M., Copsey T., Cooper J., Coulson A., Craxton M.,
RA Dear S., Du Z., Durbin R., Favello A., Fraser A., Fulton L., Gardner A.,
RA Green P., Hawkins T., Hillier L., Jier M., Johnston L., Jones M.,
RA Kershaw J., Kirsten J., Laisster N., Latreille P., Lightning J., Lloyd C.,
RA Mortimore B., O'Callaghan M., Parsons J., Percy C., Rifken L., Roopra A.,
RA Saunders D., Shownkeen R., Sims M., Smaldon N., Smith A., Smith M.,
RA Sonnhammer E., Staden R., Sulston J., Thierry-Mieg J., Thomas K.,
RA Vaudin M., Vaughan K., Waterston R., Watson A., Weinstock L.,
RA Wilkinson-Sproat J., Wohldman P.;
RT "2.2 Mb of contiguous nucleotide sequence from chromosome III of C.
RT elegans.";
RL Nature 368:32-38(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND ALTERNATIVE SPLICING.
RC STRAIN=Bristol N2;
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
CC -!- FUNCTION: DNA polymerase specifically involved in DNA repair. Plays an
CC important role in translesion synthesis, where the normal high-fidelity
CC DNA polymerases cannot proceed and DNA synthesis stalls. Depending on
CC the context, it inserts the correct base, but causes frequent base
CC transitions, transversions and frameshifts. Lacks 3'-5' proofreading
CC exonuclease activity. Forms a Schiff base with 5'-deoxyribose phosphate
CC at abasic sites, but does not have lyase activity (By similarity).
CC {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 -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Divalent metal cations. Prefers Mg(2+), but can also use Mn(2+).
CC {ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=a;
CC IsoId=P34409-1; Sequence=Displayed;
CC Name=b;
CC IsoId=P34409-2; Sequence=VSP_032729;
CC -!- DOMAIN: The catalytic core consists of fingers, palm and thumb
CC subdomains, but the fingers and thumb subdomains are much smaller than
CC in high-fidelity polymerases; residues from five sequence motifs of the
CC Y-family cluster around an active site cleft that can accommodate DNA
CC and nucleotide substrates with relaxed geometric constraints, with
CC consequently higher rates of misincorporation and low processivity.
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-Y family. {ECO:0000305}.
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; FO080222; CCD62142.1; -; Genomic_DNA.
DR EMBL; FO080222; CCD62143.1; -; Genomic_DNA.
DR PIR; S44637; S44637.
DR RefSeq; NP_001122692.1; NM_001129220.1. [P34409-1]
DR RefSeq; NP_001122693.1; NM_001129221.3.
DR AlphaFoldDB; P34409; -.
DR SMR; P34409; -.
DR STRING; 6239.F22B7.6a; -.
DR EPD; P34409; -.
DR PaxDb; P34409; -.
DR EnsemblMetazoa; F22B7.6a.1; F22B7.6a.1; WBGene00017696. [P34409-1]
DR EnsemblMetazoa; F22B7.6b.1; F22B7.6b.1; WBGene00017696. [P34409-2]
DR EnsemblMetazoa; F22B7.6b.2; F22B7.6b.2; WBGene00017696. [P34409-2]
DR GeneID; 176209; -.
DR KEGG; cel:CELE_F22B7.6; -.
DR UCSC; F22B7.6b.2; c. elegans. [P34409-1]
DR CTD; 176209; -.
DR WormBase; F22B7.6a; CE41638; WBGene00017696; polk-1. [P34409-1]
DR WormBase; F22B7.6b; CE41639; WBGene00017696; polk-1. [P34409-2]
DR eggNOG; KOG2094; Eukaryota.
DR GeneTree; ENSGT00940000156667; -.
DR HOGENOM; CLU_012348_11_4_1; -.
DR InParanoid; P34409; -.
DR OMA; RTQFKGR; -.
DR OrthoDB; 878533at2759; -.
DR PhylomeDB; P34409; -.
DR Reactome; R-CEL-5655862; Translesion synthesis by POLK.
DR Reactome; R-CEL-5696397; Gap-filling DNA repair synthesis and ligation in GG-NER.
DR Reactome; R-CEL-5696400; Dual Incision in GG-NER.
DR Reactome; R-CEL-6782135; Dual incision in TC-NER.
DR Reactome; R-CEL-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR PRO; PR:P34409; -.
DR Proteomes; UP000001940; Chromosome III.
DR Bgee; WBGene00017696; Expressed in germ line (C elegans) and 4 other tissues.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003684; F:damaged DNA binding; IEA:InterPro.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR GO; GO:0009792; P:embryo development ending in birth or egg hatching; IGI:WormBase.
DR GO; GO:0042276; P:error-prone translesion synthesis; IMP:WormBase.
DR GO; GO:0000003; P:reproduction; IGI:WormBase.
DR GO; GO:0019985; P:translesion synthesis; IMP:WormBase.
DR CDD; cd03586; PolY_Pol_IV_kappa; 1.
DR Gene3D; 3.30.1490.100; -; 1.
DR Gene3D; 3.30.70.270; -; 1.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR036775; DNA_pol_Y-fam_lit_finger_sf.
DR InterPro; IPR017961; DNA_pol_Y-fam_little_finger.
DR InterPro; IPR022880; DNApol_IV.
DR InterPro; IPR024728; PolY_HhH_motif.
DR InterPro; IPR006642; Rad18_UBZ4.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR InterPro; IPR001126; UmuC.
DR Pfam; PF00817; IMS; 1.
DR Pfam; PF11799; IMS_C; 1.
DR Pfam; PF11798; IMS_HHH; 1.
DR SUPFAM; SSF100879; SSF100879; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS50173; UMUC; 1.
DR PROSITE; PS51908; ZF_UBZ4; 1.
PE 3: Inferred from homology;
KW Alternative splicing; DNA damage; DNA repair; DNA replication;
KW DNA synthesis; DNA-directed DNA polymerase; Magnesium; Metal-binding;
KW Mutator protein; Nucleotidyltransferase; Nucleus; Reference proteome;
KW Schiff base; Transferase; Zinc; Zinc-finger.
FT CHAIN 1..596
FT /note="DNA polymerase kappa"
FT /id="PRO_0000173996"
FT DOMAIN 85..320
FT /note="UmuC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00216"
FT ZN_FING 516..545
FT /note="UBZ4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01256"
FT REGION 559..584
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 181
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00216"
FT BINDING 89
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00216"
FT BINDING 180
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00216"
FT BINDING 519
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01256"
FT BINDING 522
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01256"
FT BINDING 536
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01256"
FT BINDING 540
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01256"
FT SITE 94
FT /note="Substrate discrimination"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00216"
FT VAR_SEQ 1..133
FT /note="Missing (in isoform b)"
FT /evidence="ECO:0000305"
FT /id="VSP_032729"
SQ SEQUENCE 596 AA; 67942 MW; 48946E0994339523 CRC64;
MLTFNDNKAG MNGLDKEKIT KVIEENTSAS YSSFSKKQQS RIEEKVLEIK NRLQTATREE
RQKSEILMEN LEMKLESSRD LSRDCVCIDM DAYFAAVEMR DNPALRTVPM AVGSSAMLST
SNYLARRFGV RAGMPGFISN KLCPSLTIVP GNYPKYTKVS RQFSQIFMEY DSDVGMMSLD
EAFIDLTDYV ASNTEKKTFK RHRFGGDCPC WLPRFDENEN TLEDLKIEES ICPKCEKSRK
IYYDHVEFGT GREEAVREIR FRVEQLTGLT CSAGIASNFM LAKICSDLNK PNGQYVLEND
KNAIMEFLKD LPIRKVGGIG RVCEAQLKAM DIQTVGDMNL KKNLYPLCFT PLSQESFLRT
ALGLPGRPSE SDPRRKSISV ERTFSPTSDF NILLEEHQEI CRMLEEDVRK SGIVGGKTVT
LKLKLSSFDV LTRSLTPSDV VKSLEDIQKF SLELLEKEKG KEIRLLGVRL SQLIFEEDEK
KRSKTITEFW NEKKLQIQNL QGSENVDDDD VIMMDTRPCP ICGTDVENRL DVMNCHVDEC
ILKVQNDDGP ELICVSVENK STQKPERPST KKRKLQEKRP KAKKMVTIDS FWKKSG
