DPOD1_ARATH
ID DPOD1_ARATH Reviewed; 1095 AA.
AC Q9LVN7; A0MA44;
DT 21-FEB-2001, integrated into UniProtKB/Swiss-Prot.
DT 08-FEB-2011, sequence version 2.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=DNA polymerase delta catalytic subunit;
DE EC=2.7.7.7;
DE AltName: Full=Protein EMBRYO DEFECTIVE 2780;
GN Name=POLD1; Synonyms=EMB2780; OrderedLocusNames=At5g63960;
GN ORFNames=MBM17.6;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=19789281; DOI=10.1105/tpc.109.069682;
RA Schuermann D., Fritsch O., Lucht J.M., Hohn B.;
RT "Replication stress leads to genome instabilities in Arabidopsis DNA
RT polymerase delta mutants.";
RL Plant Cell 21:2700-2714(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
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 -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9LVN7-1; Sequence=Displayed;
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=BAA96899.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB019227; BAA96899.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED97821.1; -; Genomic_DNA.
DR EMBL; DQ160246; ABA41487.1; -; mRNA.
DR RefSeq; NP_201201.2; NM_125792.2. [Q9LVN7-1]
DR AlphaFoldDB; Q9LVN7; -.
DR SMR; Q9LVN7; -.
DR BioGRID; 21759; 4.
DR IntAct; Q9LVN7; 2.
DR STRING; 3702.AT5G63960.2; -.
DR PaxDb; Q9LVN7; -.
DR PRIDE; Q9LVN7; -.
DR ProteomicsDB; 241250; -. [Q9LVN7-1]
DR EnsemblPlants; AT5G63960.1; AT5G63960.1; AT5G63960. [Q9LVN7-1]
DR GeneID; 836517; -.
DR Gramene; AT5G63960.1; AT5G63960.1; AT5G63960. [Q9LVN7-1]
DR KEGG; ath:AT5G63960; -.
DR Araport; AT5G63960; -.
DR eggNOG; KOG0969; Eukaryota.
DR InParanoid; Q9LVN7; -.
DR OMA; GNQKSPY; -.
DR PhylomeDB; Q9LVN7; -.
DR BRENDA; 2.7.7.7; 399.
DR PRO; PR:Q9LVN7; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LVN7; baseline and differential.
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; Alternative splicing; DNA replication; DNA-binding;
KW DNA-directed DNA polymerase; Exonuclease; Hydrolase; Iron; Iron-sulfur;
KW Metal-binding; Nuclease; Nucleotidyltransferase; Nucleus;
KW Reference proteome; Transferase; Zinc; Zinc-finger.
FT CHAIN 1..1095
FT /note="DNA polymerase delta catalytic subunit"
FT /id="PRO_0000046449"
FT ZN_FING 1007..1023
FT /note="CysA-type"
FT REGION 1..37
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 1052..1070
FT /note="CysB motif"
FT BINDING 1007
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1010
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1020
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1023
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1052
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 1055
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 1070
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1095 AA; 123236 MW; 08FDA368381198F1 CRC64;
MNRSGISKKR PPPSNTPPPA GKHRATGDST PSPAIGTLDD EFMMEEDVFL DETLLYGDED
EESLILRDIE ERESRSSAWA RPPLSPAYLS NSQSIIFQQL EIDSIIAESH KELLPGSSGQ
APIIRMFGVT REGNSVCCFV HGFEPYFYIA CPPGMGPDDI SNFHQSLEGR MRESNKNAKV
PKFVKRIEMV QKRSIMYYQQ QKSQTFLKIT VALPTMVASC RGILDRGLQI DGLGMKSFQT
YESNILFVLR FMVDCDIVGG NWIEVPTGKY KKNARTLSYC QLEFHCLYSD LISHAAEGEY
SKMAPFRVLS FDIECAGRKG HFPEAKHDPV IQIANLVTLQ GEDHPFVRNV MTLKSCAPIV
GVDVMSFETE REVLLAWRDL IRDVDPDIII GYNICKFDLP YLIERAATLG IEEFPLLGRV
KNSRVRVRDS TFSSRQQGIR ESKETTIEGR FQFDLIQAIH RDHKLSSYSL NSVSAHFLSE
QKEDVHHSII TDLQNGNAET RRRLAVYCLK DAYLPQRLLD KLMFIYNYVE MARVTGVPIS
FLLARGQSIK VLSQLLRKGK QKNLVLPNAK QSGSEQGTYE GATVLEARTG FYEKPIATLD
FASLYPSIMM AYNLCYCTLV TPEDVRKLNL PPEHVTKTPS GETFVKQTLQ KGILPEILEE
LLTARKRAKA DLKEAKDPLE KAVLDGRQLA LKISANSVYG FTGATVGQLP CLEISSSVTS
YGRQMIEQTK KLVEDKFTTL GGYQYNAEVI YGDTDSVMVQ FGVSDVEAAM TLGREAAEHI
SGTFIKPIKL EFEKVYFPYL LINKKRYAGL LWTNPQQFDK MDTKGIETVR RDNCLLVKNL
VTESLNKILI DRDVPGAAEN VKKTISDLLM NRIDLSLLVI TKGLTKTGDD YEVKSAHGEL
AERMRKRDAA TAPNVGDRVP YVIIKAAKGA KAYERSEDPI YVLQNNIPID PNYYLENQIS
KPLLRIFEPV LKNASKELLH GSHTRSISIT TPSNSGIMKF AKKQLSCVGC KVPISNGTLC
ASCKGREAEL YCKNVSQVAE LEEVFGRLWT QCQECQGSLH QDVLCTSRDC PIFYRRMKAQ
KDMAVARQQL DRWSF
