ID   DPOD1_ORYSJ             Reviewed;        1105 AA.
AC   Q9LRE6; A0A0N7KSJ4; Q2R9L5; Q53NH0; Q53P50;
DT   21-FEB-2001, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   03-AUG-2022, entry version 141.
DE   RecName: Full=DNA polymerase delta catalytic subunit;
DE            EC=2.7.7.7;
GN   Name=POLD1; OrderedLocusNames=Os11g0186400, LOC_Os11g08330;
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RA   Hatanaka M., Kimura S., Sakaguti K.;
RT   "Oryza sativa DNA polymerase delta catalytic chain.";
RL   Submitted (FEB-2000) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16188032; DOI=10.1186/1741-7007-3-20;
RG   The rice chromosomes 11 and 12 sequencing consortia;
RT   "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT   genes and recent gene duplications.";
RL   BMC Biol. 3:20-20(2005).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [4]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [5]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
CC   -!- FUNCTION: This polymerase possesses two enzymatic activities: DNA
CC       synthesis (polymerase) and an exonucleolytic activity that degrades
CC       single-stranded DNA in the 3'- to 5'-direction.
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: Heterodimer with subunits of 125 kDa and 50 kDa. The 125 kDa
CC       subunit contains the polymerase active site and most likely the active
CC       site for the 3'-5' exonuclease activity (By 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   -!- MISCELLANEOUS: In eukaryotes there are five DNA polymerases: alpha,
CC       beta, gamma, delta, and epsilon which are responsible for different
CC       reactions of DNA synthesis.
CC   -!- SIMILARITY: Belongs to the DNA polymerase type-B family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAY23282.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AB037899; BAA99573.1; -; mRNA.
DR   EMBL; AC128644; AAX96341.1; -; Genomic_DNA.
DR   EMBL; AC134047; AAY23282.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; DP000010; ABA91815.1; -; Genomic_DNA.
DR   EMBL; AP008217; BAF27768.1; -; Genomic_DNA.
DR   EMBL; AP014967; BAT12986.1; -; Genomic_DNA.
DR   RefSeq; XP_015617044.1; XM_015761558.1.
DR   AlphaFoldDB; Q9LRE6; -.
DR   SMR; Q9LRE6; -.
DR   STRING; 4530.OS11T0186400-00; -.
DR   PaxDb; Q9LRE6; -.
DR   PRIDE; Q9LRE6; -.
DR   EnsemblPlants; Os11t0186400-00; Os11t0186400-00; Os11g0186400.
DR   GeneID; 4349968; -.
DR   Gramene; Os11t0186400-00; Os11t0186400-00; Os11g0186400.
DR   KEGG; osa:4349968; -.
DR   eggNOG; KOG0969; Eukaryota.
DR   HOGENOM; CLU_000203_2_0_1; -.
DR   InParanoid; Q9LRE6; -.
DR   OMA; GNQKSPY; -.
DR   OrthoDB; 20210at2759; -.
DR   PlantReactome; R-OSA-9675782; Maturation.
DR   PlantReactome; R-OSA-9675815; Leading strand synthesis.
DR   PlantReactome; R-OSA-9675885; Lagging strand synthesis.
DR   Proteomes; UP000000763; Chromosome 11.
DR   Proteomes; UP000059680; Chromosome 11.
DR   Genevisible; Q9LRE6; OS.
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; IBA:GO_Central.
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: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   2: Evidence at transcript level;
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..1105
FT                   /note="DNA polymerase delta catalytic subunit"
FT                   /id="PRO_0000046450"
FT   ZN_FING         1015..1033
FT                   /note="CysA-type"
FT   REGION          1..46
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           1062..1080
FT                   /note="CysB motif"
FT   BINDING         1015
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250"
FT   BINDING         1018
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         1033
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250"
FT   BINDING         1062
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000250"
FT   BINDING         1065
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000250"
FT   BINDING         1075
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000250"
FT   BINDING         1080
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   1105 AA;  123757 MW;  C309447C049D42C1 CRC64;
     MSSGGRGGKR RGAPPPGPSG AAAKRAHPGG TPQPPPPAAT AAAPVAEEED MMDEDVFLDE
     TILAEDEEAL LLLDRDEALA SRLSRWRRPA LPADLASGCS RNVAFQQLEI DYVIGESHKV
     LLPNSSGPAA ILRIFGVTRE GHSVCCQVHG FEPYFYISCP MGMGPDDISR FHQTLEGRMK
     DSNRNSNVPR FVKRIELVQK QTIMHYQPQQ SQPFLKIVVA LPTMVASCRG ILERGITIEG
     LGSKSFLTYE SNILFALRFM IDCNIVGGNW IEVPAGKYMK AARIMSYCQL ELDCLYSDLV
     SHAAEGEHSK MAPFRILSFD IECAGRKGHF PEPTHDPVIQ IANLVTLQGE GQPFVRNVMT
     LKSCSPIVGV DVMSFDTERD VLLAWRDFIR EVDPDIIIGY NICKFDLPYL IERAEVLKIV
     EFPILGRIRN SRVRVRDTTF SSRQYGMRES KDVAVEGRVQ FDLLQAMQRD YKLSSYSLNS
     VSAHFLGEQK EDVHHSIISD LQNGNSETRR RLAVYCLKDA YLPQRLLDKL MYIYNYVEMA
     RVTGVPISFL LSRGQSIKVL SQLLRKAKQK NLVIPNIKGQ ASGQDTFEGA TVLEARAGFY
     EKPIATLDFA SLYPSIMMAY NLCYCTLVPP EDARKLNLPP ESVNKTPSGE TFVKPDVQKG
     ILPEILEELL AARKRAKADL KEAKDPFERA VLDGRQLALK ISANSVYGFT GATVGQLPCL
     EISSSVTSYG RQMIEHTKKL VEDKFTTLGG YEHNAEVIYG DTDSVMVQFG VSTVEDAMKL
     GREAADYISG TFIKPIKLEF EKIYFPYLLI SKKRYAGLYW TNPEKFDKMD TKGIETVRRD
     NCLLVKNLVT ECLHKILVDR DVPGAVQYVK NTISDLLMNR VDLSLLVITK GLTKTGEDYA
     VKAAHVELAE RMRKRDAATA PTVGDRVPYV IIKAAKGAKA YERSEDPIYV LDNNIPIDPQ
     YYLENQISKP LLRIFEPILK NASRELLHGS HTRAVSISTP SNSGIMKFAK KQLTCLGCKA
     VISGSNQTLC FHCKGREAEL YCKTVGNVSE LEMLFGRLWT QCQECQGSLH QDVLCTSRDC
     PIFYRRRKAQ KDMAEARVQL QRWDF