PAPS3_ARATH
ID PAPS3_ARATH Reviewed; 507 AA.
AC Q56XM9; Q7XJ92; Q9C8Z7;
DT 26-NOV-2014, integrated into UniProtKB/Swiss-Prot.
DT 10-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=Nuclear poly(A) polymerase 3 {ECO:0000303|PubMed:18479511};
DE Short=PAP(III) {ECO:0000305};
DE Short=Poly(A) polymerase III {ECO:0000305};
DE EC=2.7.7.19 {ECO:0000269|PubMed:15297145};
DE AltName: Full=Polynucleotide adenylyltransferase 3 {ECO:0000305};
GN Name=PAPS3 {ECO:0000303|PubMed:18479511};
GN OrderedLocusNames=At3g06560 {ECO:0000312|Araport:AT3G06560};
GN ORFNames=F5E6.11 {ECO:0000312|EMBL:AAG51325.1};
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|EMBL:BAD95301.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), 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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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;
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 (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP INTERACTION WITH FIPS5 AND CPSF30, 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 [6]
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) subunits FIPS5 and CPSF30
CC (PubMed:18479511). {ECO:0000250|UniProtKB:P25500,
CC ECO:0000269|PubMed:18479511}.
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=Q56XM9-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q56XM9-2; Sequence=VSP_057245;
CC -!- TISSUE SPECIFICITY: Expressed in leaves (mostly in petioles and tips),
CC cotyledon, roots (tips, vascular tissue of the radicle, and throughout
CC the root tissue excluding the elongation zone), stems, and flowers
CC (restricted to the stigma and the pollen in mature anthers)
CC (PubMed:15297145, PubMed:19956626). Active in the primary and secondary
CC root systems (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; AY323907; AAP86215.1; -; mRNA.
DR EMBL; AC020580; AAG51325.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74415.1; -; Genomic_DNA.
DR EMBL; AK221644; BAD95301.1; -; mRNA.
DR RefSeq; NP_187308.3; NM_111532.3. [Q56XM9-1]
DR AlphaFoldDB; Q56XM9; -.
DR SMR; Q56XM9; -.
DR BioGRID; 5170; 3.
DR IntAct; Q56XM9; 4.
DR STRING; 3702.AT3G06560.1; -.
DR iPTMnet; Q56XM9; -.
DR PaxDb; Q56XM9; -.
DR PRIDE; Q56XM9; -.
DR ProteomicsDB; 236353; -. [Q56XM9-1]
DR EnsemblPlants; AT3G06560.1; AT3G06560.1; AT3G06560. [Q56XM9-1]
DR GeneID; 819835; -.
DR Gramene; AT3G06560.1; AT3G06560.1; AT3G06560. [Q56XM9-1]
DR KEGG; ath:AT3G06560; -.
DR Araport; AT3G06560; -.
DR TAIR; locus:2084274; AT3G06560.
DR eggNOG; KOG2245; Eukaryota.
DR HOGENOM; CLU_011511_6_0_1; -.
DR InParanoid; Q56XM9; -.
DR OMA; QWPTPVV; -.
DR OrthoDB; 326577at2759; -.
DR PhylomeDB; Q56XM9; -.
DR BRENDA; 2.7.7.19; 399.
DR PRO; PR:Q56XM9; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q56XM9; baseline and differential.
DR Genevisible; Q56XM9; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
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:0006378; P:mRNA polyadenylation; IBA:GO_Central.
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; IPR014492; PolyA_polymerase.
DR Pfam; PF04928; PAP_central; 1.
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..507
FT /note="Nuclear poly(A) polymerase 3"
FT /id="PRO_0000431347"
FT BINDING 79..81
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 91..94
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P29468"
FT BINDING 92
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 92
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 94
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 94
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 147
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 147
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 208
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 217
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 226..227
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT SITE 368
FT /note="Interaction with RNA"
FT /evidence="ECO:0000250|UniProtKB:P29468"
FT SITE 373
FT /note="Interaction with RNA"
FT /evidence="ECO:0000250|UniProtKB:P29468"
FT VAR_SEQ 1..24
FT /note="Missing (in isoform 2)"
FT /id="VSP_057245"
FT CONFLICT 107
FT /note="Missing (in Ref. 2; AAG51325)"
FT CONFLICT 180
FT /note="I -> S (in Ref. 1; AAP86215)"
FT CONFLICT 258
FT /note="H -> L (in Ref. 1; AAP86215)"
SQ SEQUENCE 507 AA; 57704 MW; 11EBB2C0995490C6 CRC64;
MKKGGGRNKG FPQDDESSIS LRQLMVNEGL IPSLEDEVKR RGVINQLRKI VVRWVKNVAW
QHRLPQNQID ATNATILPYG SYGLGVYGSE SDIDALCIGP FFASIAEDFF ISLRDMLKSR
REVSELHCVK DAKVPLIRFK FDGILVDLPY AQLRVLSIPN NVDVLNPFFL RDIDETSWKI
LSGVRANKCI LQLVPSLELF QSLLRCVKLW AKRRGVYGNL NGFLGGVHMA ILAAFVCGYQ
PNATLSSLLA NFFYTFAHWQ WPTPVVLLED TYPSTGAPPG LMPIQLPCGS HQYCNSTITR
STFYKIVAEF LLGHNLTKDY LKLNFSWKDL FELYPYANTY TWFTKIHLSA ANQEDLSDWV
GWVKSRFRCL LIKIEEVYGI CDPNPTEYVE TYTKQPNIVF YWGLQLRTIN VSDIESVKID
FLKNVNSGSF RGTVGRIQLT LVKASQLPKN GECGSNNRSK KVTKTCWRIR EDKQCNNVPV
YSKHLPGYVV GYQKMVNREA DGMEVKC
