PAPS2_ARATH
ID PAPS2_ARATH Reviewed; 800 AA.
AC O82312; F4ISP7; F4ISP8; F4ISP9; Q94BP6; Q9LKX0;
DT 26-NOV-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 2.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=Nuclear poly(A) polymerase 2 {ECO:0000303|PubMed:18479511};
DE Short=PAP(II) {ECO:0000305};
DE Short=Poly(A) polymerase II {ECO:0000305};
DE EC=2.7.7.19 {ECO:0000269|PubMed:15297145};
DE AltName: Full=Polynucleotide adenylyltransferase 2 {ECO:0000305};
GN Name=PAPS2 {ECO:0000303|PubMed:18479511};
GN OrderedLocusNames=At2g25850 {ECO:0000312|Araport:AT2G25850};
GN ORFNames=F17H15.12 {ECO:0000312|EMBL:AAC42245.2};
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), AND FUNCTION.
RX PubMed=10872823; DOI=10.1006/bbrc.2000.2755;
RA Hunt A.G., Meeks L.R., Forbes K.P., Das Gupta J., Mogen B.D.;
RT "Nuclear and chloroplast poly(A) polymerases from plants share a novel
RT biochemical property.";
RL Biochem. Biophys. Res. Commun. 272:174-181(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
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 ALTERNATIVE SPLICING, FUNCTION, CATALYTIC ACTIVITY, TISSUE SPECIFICITY,
RP 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 [6]
RP INTERACTION WITH CPSF100; CPSF30; FIPS5 AND PABN2, GENE FAMILY, AND
RP 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). Mediates the polyadenylation of RNAs that are associated
CC with polynucleotide phosphorylase (e.g. PNP1) (PubMed:10872823).
CC {ECO:0000250|UniProtKB:P25500, ECO:0000269|PubMed:15297145,
CC ECO:0000269|PubMed:19956626, ECO:0000305|PubMed:10872823}.
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 CPSF100, CPSF30,
CC FIPS5 and PABN2 (PubMed:18479511). {ECO:0000250|UniProtKB:P25500,
CC ECO:0000269|PubMed:18479511}.
CC -!- INTERACTION:
CC O82312; Q9LKF9: CPSF100; NbExp=5; IntAct=EBI-1775513, EBI-1775444;
CC O82312; A9LNK9: CPSF30; NbExp=3; IntAct=EBI-1775513, EBI-962511;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P25500,
CC ECO:0000255|PROSITE-ProRule:PRU00768}. Cytoplasm
CC {ECO:0000269|PubMed:19956626}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=5;
CC Name=1;
CC IsoId=O82312-1; Sequence=Displayed;
CC Name=2;
CC IsoId=O82312-2; Sequence=VSP_057242;
CC Name=3;
CC IsoId=O82312-3; Sequence=VSP_057240, VSP_057244;
CC Name=4;
CC IsoId=O82312-4; Sequence=VSP_057241, VSP_057243;
CC Name=5;
CC IsoId=O82312-5; Sequence=VSP_057239;
CC -!- TISSUE SPECIFICITY: Mostly expressed in flowers (highly in the style,
CC receptacle and pedicel, but weakly in the vasculature of sepals) and
CC hypocotyls, and, to a lower extent, in roots and stems. Barely detected
CC in leaves (petioles and vascular system) (PubMed:15297145,
CC 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; AF255297; AAF66438.2; -; mRNA.
DR EMBL; AC005395; AAC42245.2; -; Genomic_DNA.
DR EMBL; CP002685; AEC07761.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC07762.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC07763.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC07764.1; -; Genomic_DNA.
DR EMBL; AY039974; AAK64151.1; -; mRNA.
DR EMBL; AY074533; AAL69501.1; -; mRNA.
DR PIR; E84653; E84653.
DR RefSeq; NP_001031417.1; NM_001036340.1. [O82312-4]
DR RefSeq; NP_001189603.1; NM_001202674.2. [O82312-2]
DR RefSeq; NP_565611.1; NM_128145.4. [O82312-1]
DR RefSeq; NP_850071.1; NM_179740.2. [O82312-3]
DR AlphaFoldDB; O82312; -.
DR SMR; O82312; -.
DR BioGRID; 2479; 3.
DR IntAct; O82312; 6.
DR STRING; 3702.AT2G25850.2; -.
DR PaxDb; O82312; -.
DR PRIDE; O82312; -.
DR ProteomicsDB; 248638; -. [O82312-1]
DR EnsemblPlants; AT2G25850.1; AT2G25850.1; AT2G25850. [O82312-3]
DR EnsemblPlants; AT2G25850.2; AT2G25850.2; AT2G25850. [O82312-1]
DR EnsemblPlants; AT2G25850.3; AT2G25850.3; AT2G25850. [O82312-4]
DR EnsemblPlants; AT2G25850.4; AT2G25850.4; AT2G25850. [O82312-2]
DR GeneID; 817127; -.
DR Gramene; AT2G25850.1; AT2G25850.1; AT2G25850. [O82312-3]
DR Gramene; AT2G25850.2; AT2G25850.2; AT2G25850. [O82312-1]
DR Gramene; AT2G25850.3; AT2G25850.3; AT2G25850. [O82312-4]
DR Gramene; AT2G25850.4; AT2G25850.4; AT2G25850. [O82312-2]
DR KEGG; ath:AT2G25850; -.
DR Araport; AT2G25850; -.
DR TAIR; locus:2043560; AT2G25850.
DR eggNOG; KOG2245; Eukaryota.
DR InParanoid; O82312; -.
DR PhylomeDB; O82312; -.
DR BRENDA; 2.7.7.19; 399.
DR PRO; PR:O82312; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; O82312; baseline and differential.
DR Genevisible; O82312; AT.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
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:0006378; P:mRNA polyadenylation; IBA:GO_Central.
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; IPR002934; Polymerase_NTP_transf_dom.
DR Pfam; PF01909; NTP_transf_2; 1.
DR Pfam; PF04928; PAP_central; 1.
DR Pfam; PF04926; PAP_RNA-bind; 1.
DR SUPFAM; SSF55003; SSF55003; 1.
DR SUPFAM; SSF81301; SSF81301; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; ATP-binding; Cytoplasm; Magnesium; Metal-binding;
KW mRNA processing; Nucleotide-binding; Nucleotidyltransferase; Nucleus;
KW Reference proteome; Repeat; Transferase.
FT CHAIN 1..800
FT /note="Nuclear poly(A) polymerase 2"
FT /id="PRO_0000431346"
FT REGION 497..576
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 487..494
FT /note="Nuclear localization signal 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 533..540
FT /note="Nuclear localization signal 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 528..555
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 559..576
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 103..105
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 115..118
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P29468"
FT BINDING 116
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 116
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 118
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 118
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 171
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 171
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 232
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 241
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT BINDING 250..251
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P25500"
FT SITE 162
FT /note="Interaction with RNA"
FT /evidence="ECO:0000250|UniProtKB:P29468"
FT SITE 332
FT /note="Interaction with RNA"
FT /evidence="ECO:0000250|UniProtKB:P29468"
FT SITE 403
FT /note="Interaction with RNA"
FT /evidence="ECO:0000250|UniProtKB:P29468"
FT SITE 408
FT /note="Interaction with RNA"
FT /evidence="ECO:0000250|UniProtKB:P29468"
FT SITE 616
FT /note="Interaction with RNA"
FT /evidence="ECO:0000250|UniProtKB:P29468"
FT VAR_SEQ 223..244
FT /note="HFRTTLRCLKYWAKKRGVYSNV -> MPEVLG (in isoform 5)"
FT /id="VSP_057239"
FT VAR_SEQ 777..787
FT /note="RSESLQNEMMR -> SSRRLSLKSVA (in isoform 3)"
FT /id="VSP_057240"
FT VAR_SEQ 777..786
FT /note="RSESLQNEMM -> SRRLSLKSVA (in isoform 4)"
FT /id="VSP_057241"
FT VAR_SEQ 787..800
FT /note="RHVFLQPIIGLCKS -> SSRRLSLKSVA (in isoform 2)"
FT /id="VSP_057242"
FT VAR_SEQ 787..800
FT /note="Missing (in isoform 4)"
FT /id="VSP_057243"
FT VAR_SEQ 788..800
FT /note="Missing (in isoform 3)"
FT /id="VSP_057244"
SQ SEQUENCE 800 AA; 90968 MW; 9EEA921EADB0BF99 CRC64;
MVSTQQRTDD DSSQPVKASL KSYGITEPLS IAGPSAADVK RNLELEKFLV DEGLYESKEE
TMRREEVVVR IDQIVKHWVK QLTRQRGYTD QMVEDANAVI FTFGSYRLGV HGPMADIDTL
CVGPSYVNRE EDFFIFFRDI LAEMEEVTEL QPVTDAHVPV MKFKFQGISI DLLYASISLL
VIPQDLDISN SSVLCDVDEQ TVRSLNGCRV ADQILKLVPN SEHFRTTLRC LKYWAKKRGV
YSNVTGFLGG VNWALLVARL CQFYPNAIPS MLVSRFFRVY TQWRWPNPVM LCAIEEDDLS
FPVWDPRKNH RDRYHLMPII TPAYPCMNSS YNVSQSTLRV MTEQFQFGNT ICQEIELNKQ
HWSSLFQQYM FFEAYKNYLQ VDVLAADAED LLAWKGWVES RFRQLTLKIE RDTNGMLMCH
PQPNEYVDTS KQFRHCAFFM GLQRADGFGG QECQQFDIRG TVDEFRQEVN MYMFWRPGMD
VHVSHVRRRQ LPSFVFPNGY KRSRQSRHQS QQCREPGDEG VGSLSDSVER YAKRKNDDEI
MNSRPEKREK RASCSLHTLD AASPDSSGIT TSGTPQIGIV PGPRAECLVT GDLVCNVTSL
PNVEVEAEKF ISKITELRKF SQYEHTSGSE QILEVDSRAL VQSYHDLAEP VAKHVRPDLS
ALLACEGGQN KEIGHDMGSE SINDTDTQHL PRRLNVNEDV DEVEREAKLG EIAGGVLWNG
HCGRNLDHEG FVTPANLDSA VENRNLHSDG LFKSGLPEEL QSNSLLSGTG KLDDGARSES
LQNEMMRHVF LQPIIGLCKS
