ID   POLIA_ORYSJ             Reviewed;        1033 AA.
AC   Q6Z4T5; A0A0P0XCJ7; Q69S01; Q8S9E2;
DT   11-JUN-2014, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2004, sequence version 1.
DT   03-AUG-2022, entry version 127.
DE   RecName: Full=DNA polymerase I A, chloroplastic;
DE            EC=2.7.7.7;
DE   AltName: Full=DNA polymerase PolI-like A;
DE            Short=OsPolI-like A;
DE   AltName: Full=DNA polymerase gamma 1;
DE   Flags: Precursor;
GN   OrderedLocusNames=Os08g0175300, LOC_Os08g07840;
GN   ORFNames=OJ1134_B10.8-1, OJ1134_B10.8-2, OsJ_26226, OSJNBa0054L03.39-1,
GN   OSJNBa0054L03.39-2;
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], FUNCTION, ACTIVITY REGULATION, SUBCELLULAR
RP   LOCATION, AND TISSUE SPECIFICITY.
RX   PubMed=11917019; DOI=10.1093/nar/30.7.1585;
RA   Kimura S., Uchiyama Y., Kasai N., Saotome A., Ueda T., Ando T.,
RA   Ishibashi T., Namekawa S., Oshige M., Furukawa T., Yamamoto T.,
RA   Hashimoto J., Sakaguchi K.;
RT   "A novel DNA polymerase homologous to Escherichia coli DNA polymerase I
RT   from a higher plant, rice (Oryza sativa L.).";
RL   Nucleic Acids Res. 30:1585-1592(2002).
RN   [2]
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   [3]
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   [4]
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).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12869764; DOI=10.1126/science.1081288;
RG   The rice full-length cDNA consortium;
RT   "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT   japonica rice.";
RL   Science 301:376-379(2003).
CC   -!- FUNCTION: In addition to polymerase activity, this DNA polymerase
CC       exhibits 5'-3' exonuclease activity (By similarity). May be required
CC       for DNA replication and accumulation in plastids. {ECO:0000250,
CC       ECO:0000269|PubMed:11917019}.
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   -!- ACTIVITY REGULATION: Inhibited by dideoxythymidine-triphosphate
CC       (ddTTP), but not by aphidicolin and N-ethylmaleimide.
CC       {ECO:0000269|PubMed:11917019}.
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC       {ECO:0000305|PubMed:11917019}.
CC   -!- TISSUE SPECIFICITY: Expressed in shoot apical meristem, root apical
CC       meristem, leaf primordia and the marginal meristem.
CC       {ECO:0000269|PubMed:11917019}.
CC   -!- SIMILARITY: Belongs to the DNA polymerase type-A family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAB40805.2; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC       Sequence=BAB40805.2; Type=Frameshift; Evidence={ECO:0000305};
CC       Sequence=BAD32974.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAD33362.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AB047689; BAB40805.2; ALT_SEQ; mRNA.
DR   EMBL; AP003882; BAD05227.1; -; Genomic_DNA.
DR   EMBL; AP003882; BAD32974.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP005164; BAD05554.1; -; Genomic_DNA.
DR   EMBL; AP005164; BAD33362.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008214; BAF23026.1; -; Genomic_DNA.
DR   EMBL; AP014964; BAT04060.1; -; Genomic_DNA.
DR   EMBL; CM000145; EEE68133.1; -; Genomic_DNA.
DR   EMBL; AK103236; BAG95967.1; -; mRNA.
DR   RefSeq; XP_015650956.1; XM_015795470.1.
DR   AlphaFoldDB; Q6Z4T5; -.
DR   SMR; Q6Z4T5; -.
DR   STRING; 4530.OS08T0175300-01; -.
DR   PaxDb; Q6Z4T5; -.
DR   PRIDE; Q6Z4T5; -.
DR   EnsemblPlants; Os08t0175300-01; Os08t0175300-01; Os08g0175300.
DR   GeneID; 4344789; -.
DR   Gramene; Os08t0175300-01; Os08t0175300-01; Os08g0175300.
DR   KEGG; osa:4344789; -.
DR   eggNOG; KOG0950; Eukaryota.
DR   HOGENOM; CLU_004638_0_0_1; -.
DR   InParanoid; Q6Z4T5; -.
DR   OMA; RIHCSIN; -.
DR   OrthoDB; 1121555at2759; -.
DR   Proteomes; UP000000763; Chromosome 8.
DR   Proteomes; UP000007752; Chromosome 8.
DR   Proteomes; UP000059680; Chromosome 8.
DR   ExpressionAtlas; Q6Z4T5; baseline and differential.
DR   Genevisible; Q6Z4T5; OS.
DR   GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR   GO; GO:0008408; F:3'-5' exonuclease activity; IEA:InterPro.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:UniProtKB.
DR   GO; GO:0006261; P:DNA-templated DNA replication; IEA:InterPro.
DR   GO; GO:0006302; P:double-strand break repair; IBA:GO_Central.
DR   Gene3D; 3.30.420.10; -; 1.
DR   InterPro; IPR002562; 3'-5'_exonuclease_dom.
DR   InterPro; IPR001098; DNA-dir_DNA_pol_A_palm_dom.
DR   InterPro; IPR043502; DNA/RNA_pol_sf.
DR   InterPro; IPR002298; DNA_polymerase_A.
DR   InterPro; IPR012337; RNaseH-like_sf.
DR   InterPro; IPR036397; RNaseH_sf.
DR   PANTHER; PTHR10133; PTHR10133; 1.
DR   Pfam; PF00476; DNA_pol_A; 1.
DR   Pfam; PF01612; DNA_pol_A_exo1; 1.
DR   PRINTS; PR00868; DNAPOLI.
DR   SMART; SM00482; POLAc; 1.
DR   SUPFAM; SSF53098; SSF53098; 1.
DR   SUPFAM; SSF56672; SSF56672; 1.
PE   2: Evidence at transcript level;
KW   Chloroplast; DNA damage; DNA repair; DNA replication; DNA-binding;
KW   DNA-directed DNA polymerase; Exonuclease; Hydrolase; Nuclease;
KW   Nucleotidyltransferase; Plastid; Reference proteome; Transferase;
KW   Transit peptide.
FT   TRANSIT         1..55
FT                   /note="Chloroplast"
FT                   /evidence="ECO:0000255"
FT   CHAIN           56..1033
FT                   /note="DNA polymerase I A, chloroplastic"
FT                   /id="PRO_0000429311"
FT   DOMAIN          321..482
FT                   /note="3'-5' exonuclease"
FT   REGION          1..32
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          104..142
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          696..1030
FT                   /note="Polymerase"
FT   COMPBIAS        124..142
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   CONFLICT        756
FT                   /note="A -> V (in Ref. 1; BAB40805)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   1033 AA;  116238 MW;  187D934EEF6C3FE1 CRC64;
     MAVAPPLPPA PARQLRRWKG SSPRPPPWLS SPFRRTRYLS RPAFAAGGRQ DYSPSSGMGV
     SKTGAFRLGL YGNLNVQSSV QEWVDETKRL FFLRTTNSVR NNITNGTTPL RVGNLRHDPS
     EDIRSSNYPS LYNQRERGPS NSIVNRHVDT DLAKHRVMYQ SAHAVPAPFS VVNNDIKPLN
     MLDGSKEEIP WHDSVTMESS LPKVSKSEKT LVVDKAIPDK KEHKRITRKV TPNFPDKASL
     STESKNARKL LATIYDKVLV VDNVESARSV VKLLTTKYKG FIHACDTEVA NIDVKEETPV
     GHGEVICFSI CSGNSDGEAD FGNGKTCIWV DVLDGGRDVL MEFAPFFEDP FIKKVWHNYS
     FDIHVIENCG IKVAGFHADT MHLARLWDSS RRTDGGYSLE GLTNDYRVMD AVLKDIPKTG
     KVSMKTIFGR KKVRKDGSEG KTISIEPVEK LQREDRELWI CYSSLDSMST LKLYESLKNK
     LEAKEWIFDD CPRGTMYDFY EEYWRPFGAL LVKMETEGVL VDRAYLSEIE KAAVTERELA
     ADKFRKWASK HCPDAKYMNV NSDNQIRQLF FGGIENRNKR GETWPQSKTF KVPNDEGIAT
     EGKKTPKSRT IKLFTIVEDL KIDMFTPTGW PSVSGDVLRS LAGKIPTDHI YKIDDGQEFD
     EDGSSLELPE QDIEDTSPYG TAYEAFGGGK KGREACHAIA ALCEVFSIDK LISGFIVPLQ
     GDRISCKEGR IHCSLNINTE TGRLSARTPN LQNQPALEKD RYKIRHAFVA APGNTLIVAD
     YGQLELRILA HLTNCKSMLE AFKAGGDFHS RTAMNMYQHV RDAVEEKKVL LEWHPQPGQD
     KPPVPLLKDA FGAERRKAKM LNFSIAYGKT AVGLSWDWKV SVREARDTLK LWYRDRKEVS
     AWQKKQKAFA LEKCEVYTLL GRSRQFPNMT HAGPGQKGHV ERAAINAPVQ GSAADVAMCA
     MLEIERNARL KELGWRLLLQ VHDEVILEGP TESAEEAKTI VVECMSKPFY GTNILKVDLA
     VDAKYAKSWY AAK