DPOLA_ORYSJ
ID DPOLA_ORYSJ Reviewed; 1534 AA.
AC O48653; A0A0P0VAW0; Q5N958;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 10-JAN-2006, sequence version 2.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=DNA polymerase alpha catalytic subunit;
DE EC=2.7.7.7;
GN OrderedLocusNames=Os01g0868300, LOC_Os01g64820; ORFNames=P0677H08.20;
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].
RC STRAIN=cv. Sasanishiki;
RX PubMed=9491803; DOI=10.1046/j.1365-2443.1997.1560354.x;
RA Yokoi M., Ito M., Izumi M., Miyazawa H., Nakai H., Hanaoka F.;
RT "Molecular cloning of the cDNA for the catalytic subunit of plant DNA
RT polymerase alpha and its cell-cycle dependent expression.";
RL Genes Cells 2:695-709(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
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=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: Polymerase alpha in a complex with DNA primase is a
CC replicative polymerase.
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 -!- SUBCELLULAR LOCATION: Nucleus {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=BAA24573.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=BAD81999.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB004461; BAA24573.1; ALT_FRAME; mRNA.
DR EMBL; AP003286; BAD81999.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014957; BAS75408.1; -; Genomic_DNA.
DR RefSeq; XP_015624973.1; XM_015769487.1.
DR AlphaFoldDB; O48653; -.
DR SMR; O48653; -.
DR STRING; 4530.OS01T0868300-01; -.
DR PaxDb; O48653; -.
DR PRIDE; O48653; -.
DR EnsemblPlants; Os01t0868300-01; Os01t0868300-01; Os01g0868300.
DR GeneID; 4325052; -.
DR Gramene; Os01t0868300-01; Os01t0868300-01; Os01g0868300.
DR KEGG; osa:4325052; -.
DR eggNOG; KOG0970; Eukaryota.
DR HOGENOM; CLU_001718_0_1_1; -.
DR InParanoid; O48653; -.
DR OMA; WLKIEDA; -.
DR OrthoDB; 293315at2759; -.
DR PlantReactome; R-OSA-9645850; Activation of pre-replication complex.
DR PlantReactome; R-OSA-9675782; Maturation.
DR PlantReactome; R-OSA-9675815; Leading strand synthesis.
DR PlantReactome; R-OSA-9675824; DNA replication Initiation.
DR PlantReactome; R-OSA-9675885; Lagging strand synthesis.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR Genevisible; O48653; OS.
DR GO; GO:0005658; C:alpha DNA polymerase:primase complex; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:Gramene.
DR GO; GO:0003682; F:chromatin binding; IBA:GO_Central.
DR GO; GO:0003896; F:DNA primase activity; IDA:Gramene.
DR GO; GO:0003688; F:DNA replication origin binding; IBA:GO_Central.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:Gramene.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0017076; F:purine nucleotide binding; IBA:GO_Central.
DR GO; GO:0019103; F:pyrimidine nucleotide binding; IBA:GO_Central.
DR GO; GO:0003697; F:single-stranded DNA binding; IBA:GO_Central.
DR GO; GO:0006270; P:DNA replication initiation; IDA:Gramene.
DR GO; GO:0006273; P:lagging strand elongation; IDA:Gramene.
DR GO; GO:0006272; P:leading strand elongation; IBA:GO_Central.
DR GO; GO:0009965; P:leaf morphogenesis; IEA:EnsemblPlants.
DR GO; GO:1902975; P:mitotic DNA replication initiation; IBA:GO_Central.
DR CDD; cd05532; POLBc_alpha; 1.
DR Gene3D; 1.10.132.60; -; 1.
DR Gene3D; 1.10.3200.20; -; 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; IPR024647; DNA_pol_a_cat_su_N.
DR InterPro; IPR042087; DNA_pol_B_thumb.
DR InterPro; IPR023211; DNA_pol_palm_dom_sf.
DR InterPro; IPR038256; Pol_alpha_znc_sf.
DR InterPro; IPR045846; POLBc_alpha.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR InterPro; IPR015088; Znf_DNA-dir_DNA_pol_B_alpha.
DR Pfam; PF12254; DNA_pol_alpha_N; 1.
DR Pfam; PF00136; DNA_pol_B; 1.
DR Pfam; PF03104; DNA_pol_B_exo1; 1.
DR Pfam; PF08996; zf-DNA_Pol; 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 DNA replication; DNA-binding; DNA-directed DNA polymerase; Metal-binding;
KW Nucleotidyltransferase; Nucleus; Reference proteome; Transferase; Zinc;
KW Zinc-finger.
FT CHAIN 1..1534
FT /note="DNA polymerase alpha catalytic subunit"
FT /id="PRO_0000046438"
FT ZN_FING 1340..1386
FT /note="CysA-type"
FT REGION 1..23
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 96..141
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 864..905
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 1422..1451
FT /note="CysB motif"
FT COMPBIAS 96..119
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 864..899
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 1340
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P09884"
FT BINDING 1343
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P09884"
FT BINDING 1383
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000305"
FT BINDING 1386
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P09884"
FT BINDING 1422
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P09884"
FT BINDING 1427
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P09884"
FT BINDING 1448
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P09884"
FT BINDING 1454
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1534 AA; 169920 MW; 20CC9E764233B3DA CRC64;
MDEGSADAGA SGRRSRARGS EAVARSAALE RLRAIRDGGA RAAAAVQVRI EAPIYDTVAE
EDYAALVARR RKDAGAFIVD DDGLGYADDG REEDWTHRTI HSSSDEGSDG EDGAPRKRKQ
PRPQSKRPPQ QSAAAASLSA AAAMMGKQRL SSMFTSSVFR KPGSDRGRDS SLAADSIVDD
VIAEFAPDDN DREERRRRVG RVCAPAPAPT TTAHIKAENV AVDTAMAFRS DNVFEAHEVS
DHGNDMDMEL KPDVEMEPKL DTPLGASAEL ANNSNSLEEP KQEANGEVKI EKVHRLNAKI
KTEDSRNGDM ASATAGWMKI CGDGDNAGGE GAVAANSNTG VDESSEFELK DGALPFYILD
AYEEPFGANS GTVYLFGKVE VGKRFHSCCV VVKNMQRCIY AIPSSSIFPR DTISRLEKNS
TTSDSSPSLR ASLHELASGL KSEIADKLSD FNVSNFAMTP VKRNYAFERT DLPNGEQYVL
KINYPYKDPA LPTDLRGQHF HALLGTNNSA LELLLIKRKI KGPSWLSISK FLACPATQRV
SWCKFEVTVD SPKDISVLMT STTLEVPPVV VAAVNLKTII NEKHNVHEIV SASVICCHRV
KIDSPMRSED WQKRGMLSHF TVMRKLEGSI FPIGLSKESS DRNQKAGSNV LALESSERAL
LNRLMIELSK LDCDVLVGHN ISGFDLDVLL HRAQTCKVPS NMWSKIGRLR RSVMPRLTKG
NTLYGSGASP GIMSCIAGRL LCDTYLCSRD LLKEVSYSLT QLAETQLKKE RKEVSPHDIP
PMFQSSGALL KLVEYGETDA CLALELMFHL SVLPLTRQLT NISGNLWGKT LQGSRAQRVE
YLLLHAFHAR KFIVPDKFAR SKEFNSTKRK MNPDTEAARP DEADPSIDDE GHHVDQGKTK
KGPSYAGGLV LEPKKGLYDK YVLLLDFNSL YPSIIQEYNI CFTTVDRSAD GNVPNLPASK
TTGVLPELLK SLVERRRMVK SWLKTASGLK RQQFDIQQQA LKLTANSMYG CLGFSNSRFY
AKPLAELITL QGREILQNTV DLVQNNLNLE VIYGDTDSIM IHTGLDDISR AKGIAGKVIQ
EVNKKYRCLE IDLDGIYKRM LLLKKKKYAA IKVALDGSLR ENIERKGLDM VRRDWSLLSK
EIGDFCLNQI LSGGSCDDVI ESIHSSLVQV QEQMRGGQTE LEKYIITKSL TKAPEDYPDA
KNQPHVQVAL RLKQNGYSGC SAGDTVPYII CSQQDSESTH SGGIAQRARH PEELKRNPDK
WMIDIDYYLS QQIHPVVSRL CASIQGTSPA RLAECLGLDS SKFQSRLTES DNQDTSSMLL
SVIDDEDERY RGCEPLRLSC PSCSTTFDCP PVSSLIIGSS SGNVSNPNEG NDASINFWRR
MRCPRCPDDT DESRVSPAVL ANQMKRQADS FINLYYKGLL MCDDEGCKYS THSVNLRVMG
DSERGTICPN YPRCNGHLVR QYTEADLYRQ LSYFCYVVDA TRCLEKLDQK ARLPFEKEFA
ALSQTINLAL MEVQKIRDRC AFGWVQLKDL AISI
