PYM1_ARATH
ID PYM1_ARATH Reviewed; 204 AA.
AC Q9LPZ4; Q8LG67;
DT 07-JUN-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=Partner of Y14 and mago {ECO:0000305};
DE Short=AtPYM {ECO:0000303|PubMed:21676911};
GN Name=PYM {ECO:0000303|PubMed:16953428};
GN OrderedLocusNames=At1g11400 {ECO:0000312|Araport:AT1G11400};
GN ORFNames=T23J18.7 {ECO:0000312|EMBL:AAF16626.1};
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;
RN [1]
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 [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP INTERACTION WITH MAGO AND Y14, SUBCELLULAR LOCATION, NUCLEAR EXPORT SIGNAL,
RP AND MUTAGENESIS OF LEU-196 AND LEU-199.
RX PubMed=16953428; DOI=10.1007/s00425-006-0385-y;
RA Park N.I., Muench D.G.;
RT "Biochemical and cellular characterization of the plant ortholog of PYM, a
RT protein that interacts with the exon junction complex core proteins Mago
RT and Y14.";
RL Planta 225:625-639(2007).
RN [6]
RP INTERACTION WITH MAGO AND Y14, AND TISSUE SPECIFICITY.
RX PubMed=21676911; DOI=10.1093/jxb/err202;
RA Mufarrege E.F., Gonzalez D.H., Curi G.C.;
RT "Functional interconnections of Arabidopsis exon junction complex proteins
RT and genes at multiple steps of gene expression.";
RL J. Exp. Bot. 62:5025-5036(2011).
CC -!- FUNCTION: Key regulator of the exon junction complex (EJC), a
CC multiprotein complex that associates immediately upstream of the exon-
CC exon junction on mRNAs and serves as a positional landmark for the
CC intron exon structure of genes and directs post-transcriptional
CC processes in the cytoplasm such as mRNA export, nonsense-mediated mRNA
CC decay (NMD) or translation. Acts as an EJC disassembly factor, allowing
CC translation-dependent EJC removal and recycling by disrupting mature
CC EJC from spliced mRNAs (By similarity). Can increase in vitro the
CC expression from reporter constructs that contain leader introns
CC required for the expression of different genes. In association with
CC MAGO and PYM, participates in intron-mediated enhancement of gene
CC expression (PubMed:21676911). {ECO:0000250|UniProtKB:Q9BRP8,
CC ECO:0000269|PubMed:21676911}.
CC -!- SUBUNIT: Interacts with MAGO and Y14. {ECO:0000269|PubMed:16953428,
CC ECO:0000269|PubMed:21676911}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16953428}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:16953428}. Nucleus, nucleoplasm
CC {ECO:0000269|PubMed:16953428}. Note=Can shuttle between the nucleus and
CC the cytoplasm, but is mainly cytoplasmic.
CC {ECO:0000269|PubMed:16953428}.
CC -!- TISSUE SPECIFICITY: Expressed in root and shoot meristems, cotyledons,
CC vascular tissues of leaves, receptacle of flowers and siliques, and
CC pollen grains. {ECO:0000269|PubMed:21676911}.
CC -!- SIMILARITY: Belongs to the pym family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM61011.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AC011661; AAF16626.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE28730.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE28731.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE28732.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59814.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59815.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59816.1; -; Genomic_DNA.
DR EMBL; BT004216; AAO42233.1; -; mRNA.
DR EMBL; BT005041; AAO50574.1; -; mRNA.
DR EMBL; AY084438; AAM61011.1; ALT_INIT; mRNA.
DR PIR; H86247; H86247.
DR RefSeq; NP_001031023.1; NM_001035946.2.
DR RefSeq; NP_001322144.1; NM_001331983.1.
DR RefSeq; NP_001322145.1; NM_001331981.1.
DR RefSeq; NP_001322146.1; NM_001331982.1.
DR RefSeq; NP_563890.1; NM_101013.1.
DR RefSeq; NP_849639.1; NM_179308.4.
DR AlphaFoldDB; Q9LPZ4; -.
DR SMR; Q9LPZ4; -.
DR STRING; 3702.AT1G11400.2; -.
DR PaxDb; Q9LPZ4; -.
DR PRIDE; Q9LPZ4; -.
DR ProteomicsDB; 226015; -.
DR EnsemblPlants; AT1G11400.1; AT1G11400.1; AT1G11400.
DR EnsemblPlants; AT1G11400.2; AT1G11400.2; AT1G11400.
DR EnsemblPlants; AT1G11400.3; AT1G11400.3; AT1G11400.
DR EnsemblPlants; AT1G11400.4; AT1G11400.4; AT1G11400.
DR EnsemblPlants; AT1G11400.5; AT1G11400.5; AT1G11400.
DR EnsemblPlants; AT1G11400.6; AT1G11400.6; AT1G11400.
DR GeneID; 837682; -.
DR Gramene; AT1G11400.1; AT1G11400.1; AT1G11400.
DR Gramene; AT1G11400.2; AT1G11400.2; AT1G11400.
DR Gramene; AT1G11400.3; AT1G11400.3; AT1G11400.
DR Gramene; AT1G11400.4; AT1G11400.4; AT1G11400.
DR Gramene; AT1G11400.5; AT1G11400.5; AT1G11400.
DR Gramene; AT1G11400.6; AT1G11400.6; AT1G11400.
DR KEGG; ath:AT1G11400; -.
DR Araport; AT1G11400; -.
DR TAIR; locus:2200116; AT1G11400.
DR eggNOG; KOG4325; Eukaryota.
DR HOGENOM; CLU_074603_1_0_1; -.
DR InParanoid; Q9LPZ4; -.
DR OMA; IPGCADS; -.
DR OrthoDB; 1545729at2759; -.
DR PhylomeDB; Q9LPZ4; -.
DR PRO; PR:Q9LPZ4; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9LPZ4; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0035145; C:exon-exon junction complex; IBA:GO_Central.
DR GO; GO:0005730; C:nucleolus; IDA:TAIR.
DR GO; GO:0005654; C:nucleoplasm; IDA:TAIR.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:1903259; P:exon-exon junction complex disassembly; IBA:GO_Central.
DR GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:UniProtKB-KW.
DR GO; GO:0010628; P:positive regulation of gene expression; IEP:TAIR.
DR GO; GO:0006417; P:regulation of translation; IEA:UniProtKB-KW.
DR InterPro; IPR039333; PYM1.
DR InterPro; IPR015362; WIBG_mago-bd.
DR InterPro; IPR036348; WIBG_N_sf.
DR PANTHER; PTHR22959; PTHR22959; 1.
DR Pfam; PF09282; Mago-bind; 1.
DR SMART; SM01273; Mago-bind; 1.
DR SUPFAM; SSF101931; SSF101931; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; mRNA transport; Nonsense-mediated mRNA decay; Nucleus;
KW Reference proteome; RNA-binding; Translation regulation; Transport.
FT CHAIN 1..204
FT /note="Partner of Y14 and mago"
FT /id="PRO_0000440129"
FT REGION 1..121
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 133..153
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 195..200
FT /note="Nuclear export signal"
FT /evidence="ECO:0000269|PubMed:16953428"
FT COMPBIAS 10..48
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 104..121
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 196
FT /note="L->A: Accumulation in the nucleus; when associated
FT with A-199."
FT /evidence="ECO:0000269|PubMed:16953428"
FT MUTAGEN 199
FT /note="L->A: Accumulation in the nucleus; when associated
FT with A-196."
FT /evidence="ECO:0000269|PubMed:16953428"
SQ SEQUENCE 204 AA; 22588 MW; D02486A2AF38420A CRC64;
MGSRSGEQGK RMAELSKNLK EGERILEPTR RPDGTLRKPI RIRPGYTPED EVVKYQSKGS
LMKKEMASQG PPGYEPDPAP KPKTKAAKRN ERKKEKRLQA TAEKANSSED GSASNGSQSV
NVLASEMEAL DVSSNNDVCG GAPNPGTTGE DVEKRIRALK KKIRLTEAQQ QKTASRDLNP
EQLEKFSKLE EWRQELKALE DKAA
