PAPS1_ARATH
ID PAPS1_ARATH Reviewed; 713 AA.
AC Q9LMT2; F4I948;
DT 26-NOV-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=Nuclear poly(A) polymerase 1 {ECO:0000303|PubMed:18479511};
DE Short=PAP(I) {ECO:0000305};
DE Short=Poly(A) polymerase I {ECO:0000305};
DE EC=2.7.7.19 {ECO:0000269|PubMed:15297145};
DE AltName: Full=Polynucleotide adenylyltransferase 1 {ECO:0000305};
GN Name=PAPS1 {ECO:0000303|PubMed:18479511};
GN OrderedLocusNames=At1g17980 {ECO:0000312|Araport:AT1G17980};
GN ORFNames=F2H15.20 {ECO:0000312|EMBL:AAF97277.1};
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 {ECO:0000312|Proteomes:UP000006548};
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), ALTERNATIVE SPLICING, FUNCTION,
RP CATALYTIC ACTIVITY, TISSUE SPECIFICITY, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=15297145; DOI=10.1016/j.bbaexp.2004.06.001;
RA Addepalli B., Meeks L.R., Forbes K.P., Hunt A.G.;
RT "Novel alternative splicing of mRNAs encoding poly(A) polymerases in
RT Arabidopsis.";
RL Biochim. Biophys. Acta 1679:117-128(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP INTERACTION WITH PAPS4, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=18479511; DOI=10.1186/1471-2164-9-220;
RA Hunt A.G., Xu R., Addepalli B., Rao S., Forbes K.P., Meeks L.R., Xing D.,
RA Mo M., Zhao H., Bandyopadhyay A., Dampanaboina L., Marion A.,
RA Von Lanken C., Li Q.Q.;
RT "Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of
RT protein-protein interactions and gene expression profiling.";
RL BMC Genomics 9:220-220(2008).
RN [7]
RP FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, AND TISSUE
RP SPECIFICITY.
RX PubMed=19956626; DOI=10.1371/journal.pone.0008082;
RA Meeks L.R., Addepalli B., Hunt A.G.;
RT "Characterization of genes encoding poly(A) polymerases in plants: evidence
RT for duplication and functional specialization.";
RL PLoS ONE 4:E8082-E8082(2009).
CC -!- FUNCTION: Essential protein (PubMed:19956626). Polymerase that creates
CC the 3'-poly(A) tail of mRNA's (PubMed:15297145). Also required for the
CC endoribonucleolytic cleavage reaction at some polyadenylation sites.
CC May acquire specificity through interaction with a cleavage and
CC polyadenylation specificity factor (CPSF) at its C-terminus (By
CC similarity). {ECO:0000250|UniProtKB:P25500,
CC ECO:0000269|PubMed:15297145, ECO:0000269|PubMed:19956626}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide;
CC Xref=Rhea:RHEA:11332, Rhea:RHEA-COMP:14527, Rhea:RHEA-COMP:17347,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:140395,
CC ChEBI:CHEBI:173115; EC=2.7.7.19;
CC Evidence={ECO:0000269|PubMed:15297145};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P25500};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:P25500};
CC Note=Binds 2 magnesium ions. Also active with manganese.
CC {ECO:0000250|UniProtKB:P25500};
CC -!- SUBUNIT: Monomer (By similarity). Forms a complex with cleavage and
CC polyadenylation specificity factor (CPSF) subunit PAPS4
CC (PubMed:18479511). {ECO:0000250|UniProtKB:P25500,
CC ECO:0000269|PubMed:18479511}.
CC -!- INTERACTION:
CC Q9LMT2; Q9LEZ3: BIM1; NbExp=3; IntAct=EBI-1775760, EBI-617095;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768,
CC ECO:0000269|PubMed:19956626}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9LMT2-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9LMT2-2; Sequence=VSP_057238;
CC -!- TISSUE SPECIFICITY: Expressed in stems, cotyledons, hypocotyls,
CC radicle, leaves, and, to a lower extent, in roots (including primary
CC and secondary roots as well as root tips) and flowers (PubMed:15297145,
CC PubMed:19956626). In radicle, roots and leaves, mainly present in
CC vascular tissues (PubMed:19956626). {ECO:0000269|PubMed:15297145,
CC ECO:0000269|PubMed:19956626}.
CC -!- DISRUPTION PHENOTYPE: Lethal. {ECO:0000269|PubMed:19956626}.
CC -!- SIMILARITY: Belongs to the poly(A) polymerase family. {ECO:0000305}.
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DR EMBL; AY323906; AAP86214.1; -; mRNA.
DR EMBL; AC034106; AAF97277.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE29658.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE29659.1; -; Genomic_DNA.
DR EMBL; BT005990; AAO64925.1; -; mRNA.
DR EMBL; AK227446; BAE99449.1; -; mRNA.
DR PIR; B86315; B86315.
DR RefSeq; NP_173240.2; NM_101661.5. [Q9LMT2-1]
DR RefSeq; NP_973855.1; NM_202126.2. [Q9LMT2-2]
DR AlphaFoldDB; Q9LMT2; -.
DR SMR; Q9LMT2; -.
DR BioGRID; 23617; 2.
DR IntAct; Q9LMT2; 2.
DR STRING; 3702.AT1G17980.1; -.
DR iPTMnet; Q9LMT2; -.
DR PaxDb; Q9LMT2; -.
DR PRIDE; Q9LMT2; -.
DR ProteomicsDB; 236274; -. [Q9LMT2-1]
DR EnsemblPlants; AT1G17980.1; AT1G17980.1; AT1G17980. [Q9LMT2-1]
DR EnsemblPlants; AT1G17980.2; AT1G17980.2; AT1G17980. [Q9LMT2-2]
DR GeneID; 838378; -.
DR Gramene; AT1G17980.1; AT1G17980.1; AT1G17980. [Q9LMT2-1]
DR Gramene; AT1G17980.2; AT1G17980.2; AT1G17980. [Q9LMT2-2]
DR KEGG; ath:AT1G17980; -.
DR Araport; AT1G17980; -.
DR TAIR; locus:2030943; AT1G17980.
DR eggNOG; KOG2245; Eukaryota.
DR HOGENOM; CLU_011511_2_0_1; -.
DR InParanoid; Q9LMT2; -.
DR OMA; NNGQRLG; -.
DR PhylomeDB; Q9LMT2; -.
DR BRENDA; 2.7.7.19; 399.
DR PRO; PR:Q9LMT2; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9LMT2; baseline and differential.
DR Genevisible; Q9LMT2; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004652; F:polynucleotide adenylyltransferase activity; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0009908; P:flower development; IMP:TAIR.
DR GO; GO:0048366; P:leaf development; IMP:TAIR.
DR GO; GO:0006378; P:mRNA polyadenylation; IBA:GO_Central.
DR GO; GO:0008285; P:negative regulation of cell population proliferation; IMP:TAIR.
DR GO; GO:0045824; P:negative regulation of innate immune response; IMP:TAIR.
DR GO; GO:0048451; P:petal formation; IMP:TAIR.
DR GO; GO:0043631; P:RNA polyadenylation; IDA:TAIR.
DR Gene3D; 3.30.460.10; -; 1.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR011068; NuclTrfase_I-like_C.
DR InterPro; IPR007012; PolA_pol_cen_dom.
DR InterPro; IPR007010; PolA_pol_RNA-bd_dom.
DR InterPro; IPR014492; PolyA_polymerase.
DR InterPro; IPR002934; Polymerase_NTP_transf_dom.
DR Pfam; PF01909; NTP_transf_2; 1.
DR Pfam; PF04928; PAP_central; 1.
DR Pfam; PF04926; PAP_RNA-bind; 2.
DR PIRSF; PIRSF018425; PolyA_polymerase; 1.
DR SUPFAM; SSF55003; SSF55003; 1.
DR SUPFAM; SSF81301; SSF81301; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; ATP-binding; Magnesium; Metal-binding;
KW mRNA processing; Nucleotide-binding; Nucleotidyltransferase; Nucleus;
KW Reference proteome; Transferase.
FT CHAIN 1..713
FT /note="Nuclear poly(A) polymerase 1"
FT /id="PRO_0000431345"
FT REGION 480..555
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 505..531
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 532..550
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 91..93
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 103..106
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P29468"
FT BINDING 104
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 104
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 106
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 106
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 159
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 159
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 229
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 238..239
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT SITE 320
FT /note="Interaction with RNA"
FT /evidence="ECO:0000250|UniProtKB:P29468"
FT SITE 391
FT /note="Interaction with RNA"
FT /evidence="ECO:0000250|UniProtKB:P29468"
FT SITE 396
FT /note="Interaction with RNA"
FT /evidence="ECO:0000250|UniProtKB:P29468"
FT VAR_SEQ 1..127
FT /note="Missing (in isoform 2)"
FT /id="VSP_057238"
SQ SEQUENCE 713 AA; 80184 MW; 4CE3919AB3B0AB10 CRC64;
MASVQQNGQR FGVSEPISMG GPTEFDVIKT RELEKHLQDV GLYESKEEAV RREEVLGILD
QIVKTWIKTI SRAKGLNDQL LHEANAKIFT FGSYRLGVHG PGADIDTLCV GPRHATREGD
FFGELQRMLS EMPEVTELHP VPDAHVPLMG FKLNGVSIDL LYAQLPLWVI PEDLDLSQDS
ILQNADEQTV RSLNGCRVTD QILRLVPNIQ NFRTTLRCMR FWAKRRGVYS NVSGFLGGIN
WALLVARICQ LYPNALPNIL VSRFFRVFYQ WNWPNAIFLC SPDEGSLGLQ VWDPRINPKD
RLHIMPIITP AYPCMNSSYN VSESTLRIMK GEFQRGNEIC EAMESNKADW DTLFEPFAFF
EAYKNYLQID ISAANVDDLR KWKGWVESRL RQLTLKIERH FKMLHCHPHP HDFQDTSRPL
HCSYFMGLQR KQGVPAAEGE QFDIRRTVEE FKHTVNAYTL WIPGMEISVG HIKRRSLPNF
VFPGGVRPSH TSKGTWDSNR RSEHRNSSTS SAPAATTTTT EMSSESKAGS NSPVDGKKRK
WGDSETLTDQ PRNSKHIAVS VPVENCEGGS PNPSVGSICS SPMKDYCTNG KSEPISKDPP
ENVVAFSKDP PESLPIEKIA TPQAHETEEL EESFDFGNQV IEQISHKVAV LSATATIPPF
EATSNGSPFP YEAVEELEVL PTRQPDAAHR PSVQQRKPII KLSFTSLGKT NGK
