ID   DPOD1_DICDI             Reviewed;        1104 AA.
AC   Q54N97;
DT   08-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT   24-MAY-2005, sequence version 1.
DT   03-AUG-2022, entry version 111.
DE   RecName: Full=DNA polymerase delta catalytic subunit;
DE            EC=2.7.7.7;
DE   AltName: Full=DNA polymerase III;
GN   Name=pold1; ORFNames=DDB_G0285381;
OS   Dictyostelium discoideum (Slime mold).
OC   Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC   Dictyosteliaceae; Dictyostelium.
OX   NCBI_TaxID=44689;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=AX4;
RX   PubMed=15875012; DOI=10.1038/nature03481;
RA   Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA   Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA   Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA   Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA   Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA   Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA   Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA   Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA   Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA   Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA   Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA   Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA   Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA   Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA   Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA   Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA   Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT   "The genome of the social amoeba Dictyostelium discoideum.";
RL   Nature 435:43-57(2005).
CC   -!- FUNCTION: Possesses two enzymatic activities: DNA synthesis
CC       (polymerase) and an exonucleolytic activity that degrades single
CC       stranded DNA in the 3'- to 5'-direction. {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=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000250};
CC       Note=Binds 1 [4Fe-4S] cluster. {ECO:0000250};
CC   -!- SUBUNIT: Heterotetramer composed of subunits of 125 kDa, 50 kDa, 66 kDa
CC       and 12 kDa. The 125 kDa subunit contains the polymerase active site and
CC       most likely the active site for the 3'-5' exonuclease activity (By
CC       similarity). {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Nucleus.
CC   -!- DOMAIN: The CysB motif binds 1 4Fe-4S cluster and is required for the
CC       formation of polymerase complexes. {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the DNA polymerase type-B family. {ECO:0000305}.
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DR   EMBL; AAFI02000079; EAL64765.1; -; Genomic_DNA.
DR   RefSeq; XP_638283.1; XM_633191.1.
DR   AlphaFoldDB; Q54N97; -.
DR   SMR; Q54N97; -.
DR   STRING; 44689.DDB0232268; -.
DR   PaxDb; Q54N97; -.
DR   EnsemblProtists; EAL64765; EAL64765; DDB_G0285381.
DR   GeneID; 8625091; -.
DR   KEGG; ddi:DDB_G0285381; -.
DR   dictyBase; DDB_G0285381; polD1.
DR   eggNOG; KOG0969; Eukaryota.
DR   HOGENOM; CLU_000203_2_0_1; -.
DR   InParanoid; Q54N97; -.
DR   OMA; GNQKSPY; -.
DR   PhylomeDB; Q54N97; -.
DR   Reactome; R-DDI-6782135; Dual incision in TC-NER.
DR   Reactome; R-DDI-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR   Reactome; R-DDI-69091; Polymerase switching.
DR   Reactome; R-DDI-69166; Removal of the Flap Intermediate.
DR   Reactome; R-DDI-69183; Processive synthesis on the lagging strand.
DR   PRO; PR:Q54N97; -.
DR   Proteomes; UP000002195; Chromosome 4.
DR   GO; GO:0043625; C:delta DNA polymerase complex; IBA:GO_Central.
DR   GO; GO:0008296; F:3'-5'-exodeoxyribonuclease activity; IBA:GO_Central.
DR   GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003887; F:DNA-directed DNA polymerase activity; ISS:dictyBase.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR   GO; GO:0006287; P:base-excision repair, gap-filling; IBA:GO_Central.
DR   GO; GO:0006281; P:DNA repair; ISS:dictyBase.
DR   GO; GO:0045004; P:DNA replication proofreading; IBA:GO_Central.
DR   GO; GO:0006261; P:DNA-templated DNA replication; IBA:GO_Central.
DR   GO; GO:0006297; P:nucleotide-excision repair, DNA gap filling; IBA:GO_Central.
DR   Gene3D; 1.10.132.60; -; 1.
DR   Gene3D; 3.30.420.10; -; 1.
DR   Gene3D; 3.90.1600.10; -; 1.
DR   InterPro; IPR006172; DNA-dir_DNA_pol_B.
DR   InterPro; IPR017964; DNA-dir_DNA_pol_B_CS.
DR   InterPro; IPR006133; DNA-dir_DNA_pol_B_exonuc.
DR   InterPro; IPR006134; DNA-dir_DNA_pol_B_multi_dom.
DR   InterPro; IPR043502; DNA/RNA_pol_sf.
DR   InterPro; IPR042087; DNA_pol_B_thumb.
DR   InterPro; IPR023211; DNA_pol_palm_dom_sf.
DR   InterPro; IPR012337; RNaseH-like_sf.
DR   InterPro; IPR036397; RNaseH_sf.
DR   InterPro; IPR025687; Znf-C4pol.
DR   Pfam; PF00136; DNA_pol_B; 1.
DR   Pfam; PF03104; DNA_pol_B_exo1; 1.
DR   Pfam; PF14260; zf-C4pol; 1.
DR   PRINTS; PR00106; DNAPOLB.
DR   SMART; SM00486; POLBc; 1.
DR   SUPFAM; SSF53098; SSF53098; 1.
DR   SUPFAM; SSF56672; SSF56672; 1.
DR   PROSITE; PS00116; DNA_POLYMERASE_B; 1.
PE   3: Inferred from homology;
KW   4Fe-4S; DNA replication; DNA-binding; DNA-directed DNA polymerase;
KW   Exonuclease; Hydrolase; Iron; Iron-sulfur; Metal-binding; Nuclease;
KW   Nucleotidyltransferase; Nucleus; Reference proteome; Transferase; Zinc;
KW   Zinc-finger.
FT   CHAIN           1..1104
FT                   /note="DNA polymerase delta catalytic subunit"
FT                   /id="PRO_0000328348"
FT   ZN_FING         1012..1030
FT                   /note="CysA-type"
FT   REGION          1..60
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           1059..1077
FT                   /note="CysB motif"
FT   COMPBIAS        31..60
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         1012
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250"
FT   BINDING         1015
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250"
FT   BINDING         1027
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250"
FT   BINDING         1030
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250"
FT   BINDING         1059
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000250"
FT   BINDING         1062
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000250"
FT   BINDING         1072
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000250"
FT   BINDING         1077
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   1104 AA;  125346 MW;  4A4F7ECDF9FCDDA0 CRC64;
     MKRSIVTGGG NNDKKFKAQP PPKNNYRGGG DDEEDDEFEE DDDEDEGDEF GEEEDEDDID
     VENIIASDSM DIDIQDDGSQ QLFLWSRKPV QDLVPHKKPL IFQQLEVDYT EIKEPVPGMP
     GPKVGPLPAI RLFGVTKEGN SVLCKVHGFL PYFFISCPPG FTEADCKSLK HDLNESMKMS
     SNQSNEKDIE NIVVSIDIEK KKSIMGYNPN PLSDFIRITL ILPKFVTRCR EIFESGRHHF
     TIPGQPFRQY QTYESNILFA LRFLIDKGIT GCSWIELPAN TYKLSETPVS TCQIEVDTSL
     ETIISLSDDD SPAPYRILSF DIECAGRKGV FPEPEKDPVI QISNIVKNNG DAEPFIKNIF
     TLKGCSSIVG AHVIPHKREE DLLREWRKFV IKVDPDVIIG YNIVNFDIPY LISRARQLKI
     PEFALLGRIK TTISKIKSTR FSSSNLGTRE SKEISMPGRT QFDLMQAIQR DHKLTSYSLN
     NVSAHFLKEQ KEDVHFSIIS DLQNGTDDDR RRLAVYCIKD AVLPMRLLDK LMILINYTEM
     ARVTGVPLSY LLGRGEGIKV LSQLYRKAMV ENFLIPTYKV TGKGEKFQGA IVIEPTPGFY
     DTPIATLDFT SLYPSIMMAH NLCYSTLLSA EEAKKLPPEI YTTTPFGDHF IKSDTKKGLL
     PRILEELLSA RKKAKDELKN EKDPFKRAVL DGRQLALKIS ANSVYGFTGA RVGKLPCLEI
     SRSVTSFGRE MLDKTKKIVE ERYTIANGYK HDAVIIYGDT DSVMVKFGVK TVAEAMEMGR
     DAAKFVTTTF IRPINLDFEK VYYPYLLMAK KKYAGLYWTK PDIHDRMDVK GLEMVRRDTC
     LLVRNVVSTI LKKILIEKDL KSAEEYTKSV ISDLLQNRLD LSMLVITKAL SKTQYKGKVI
     HNELARKMRA RDPATAPNLG DRVPYVVIQG SKGAPIYEKA EDPLYALEHN ILLDCQYYLD
     KQLKAPLIRI FKPIMSNPDL IFHGEHTRTI AQSTLSDNNK GFFGTLKKKK VCMNCPKELT
     DTESTTCINC QHKEASLYQT SLEKVTSLET KFSEAWTQCQ RCSGSLHQPV LCSNRDCPIF
     YMRTKVQLDL IEAKKTLNRF NVEW