PR40A_ARATH
ID PR40A_ARATH Reviewed; 958 AA.
AC B6EUA9; B3H7M9; B9DFP8; Q9LPD8; Q9MAL4;
DT 11-JUL-2012, integrated into UniProtKB/Swiss-Prot.
DT 25-NOV-2008, sequence version 1.
DT 25-MAY-2022, entry version 94.
DE RecName: Full=Pre-mRNA-processing protein 40A;
DE Short=AtPRP40a {ECO:0000303|PubMed:19467629};
GN Name=PRP40A {ECO:0000303|PubMed:19467629};
GN Synonyms=MED35_1 {ECO:0000303|PubMed:22021418}, MED35A;
GN OrderedLocusNames=At1g44910 {ECO:0000312|Araport:AT1G44910};
GN ORFNames=F27F5.2 {ECO:0000312|EMBL:AAF69150.1},
GN T12C22.20 {ECO:0000312|EMBL:AAF78276.1};
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] OF 1-826.
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=17560376; DOI=10.1016/j.molcel.2007.05.007;
RA Baeckstroem S., Elfving N., Nilsson R., Wingsle G., Bjoerklund S.;
RT "Purification of a plant mediator from Arabidopsis thaliana identifies PFT1
RT as the Med25 subunit.";
RL Mol. Cell 26:717-729(2007).
RN [5]
RP FUNCTION, INTERACTION WITH NRPB1, TISSUE SPECIFICITY, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=19467629; DOI=10.1016/j.abb.2009.01.004;
RA Kang C.H., Feng Y., Vikram M., Jeong I.S., Lee J.R., Bahk J.D., Yun D.J.,
RA Lee S.Y., Koiwa H.;
RT "Arabidopsis thaliana PRP40s are RNA polymerase II C-terminal domain-
RT associating proteins.";
RL Arch. Biochem. Biophys. 484:30-38(2009).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-387, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [7]
RP NOMENCLATURE.
RX PubMed=22021418; DOI=10.1104/pp.111.188300;
RA Mathur S., Vyas S., Kapoor S., Tyagi A.K.;
RT "The Mediator complex in plants: structure, phylogeny, and expression
RT profiling of representative genes in a dicot (Arabidopsis) and a monocot
RT (rice) during reproduction and abiotic stress.";
RL Plant Physiol. 157:1609-1627(2011).
CC -!- FUNCTION: Binds the phosphorylated C-terminal domain (CTD) of the
CC largest subunit of RNA polymerase II and functions as a scaffold for
CC RNA processing machineries (Probable). May be involved in pre-mRNA
CC splicing (Probable). {ECO:0000305|PubMed:19467629}.
CC -!- SUBUNIT: Interacts (via the WW domains) with the phosphorylated C-
CC terminal domain of NRPB1 (via CTD domain).
CC {ECO:0000269|PubMed:19467629}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=B6EUA9-1; Sequence=Displayed;
CC Name=2;
CC IsoId=B6EUA9-2; Sequence=VSP_044036, VSP_044037;
CC -!- TISSUE SPECIFICITY: Highly expressed in roots (PubMed:19467629).
CC Expressed in shoots, rosette leaves, cauline leaves, stems and flowers
CC (PubMed:19467629). {ECO:0000269|PubMed:19467629}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype, probably due to the
CC redundancy with PRP40B and PRP40C. {ECO:0000269|PubMed:19467629}.
CC -!- MISCELLANEOUS: Baeckstroem et al identified PRP40A in a Mediator
CC complex pull-down assay and suggested that PRP40A could be a plant
CC specific component of the Mediator complex (PubMed:17560376). However,
CC no experimental evidence has been brought so far to confirm this
CC hypothesis (Probable). {ECO:0000269|PubMed:17560376, ECO:0000305}.
CC -!- SIMILARITY: Belongs to the PRPF40 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF69150.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAF78276.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC007915; AAF69150.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC020576; AAF78276.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE32062.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE32063.1; -; Genomic_DNA.
DR EMBL; AK316856; BAH19565.1; -; mRNA.
DR RefSeq; NP_001117438.1; NM_001123966.1. [B6EUA9-2]
DR RefSeq; NP_175113.2; NM_103573.4. [B6EUA9-1]
DR AlphaFoldDB; B6EUA9; -.
DR SMR; B6EUA9; -.
DR BioGRID; 26282; 1.
DR STRING; 3702.AT1G44910.1; -.
DR iPTMnet; B6EUA9; -.
DR PaxDb; B6EUA9; -.
DR PRIDE; B6EUA9; -.
DR ProteomicsDB; 226408; -. [B6EUA9-1]
DR EnsemblPlants; AT1G44910.1; AT1G44910.1; AT1G44910. [B6EUA9-1]
DR EnsemblPlants; AT1G44910.2; AT1G44910.2; AT1G44910. [B6EUA9-2]
DR GeneID; 841057; -.
DR Gramene; AT1G44910.1; AT1G44910.1; AT1G44910. [B6EUA9-1]
DR Gramene; AT1G44910.2; AT1G44910.2; AT1G44910. [B6EUA9-2]
DR KEGG; ath:AT1G44910; -.
DR Araport; AT1G44910; -.
DR TAIR; locus:2194894; AT1G44910.
DR eggNOG; KOG0152; Eukaryota.
DR HOGENOM; CLU_005825_2_0_1; -.
DR InParanoid; B6EUA9; -.
DR OMA; HNVTTKE; -.
DR OrthoDB; 1112854at2759; -.
DR PhylomeDB; B6EUA9; -.
DR PRO; PR:B6EUA9; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; B6EUA9; baseline and differential.
DR Genevisible; B6EUA9; AT.
DR GO; GO:0016592; C:mediator complex; IDA:UniProtKB.
DR GO; GO:0005685; C:U1 snRNP; IBA:GO_Central.
DR GO; GO:0071004; C:U2-type prespliceosome; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0070063; F:RNA polymerase binding; IDA:TAIR.
DR GO; GO:0045292; P:mRNA cis splicing, via spliceosome; IEA:InterPro.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IBA:GO_Central.
DR GO; GO:0008380; P:RNA splicing; IDA:TAIR.
DR CDD; cd00201; WW; 2.
DR Gene3D; 1.10.10.440; -; 5.
DR InterPro; IPR002713; FF_domain.
DR InterPro; IPR036517; FF_domain_sf.
DR InterPro; IPR039726; Prp40-like.
DR InterPro; IPR001202; WW_dom.
DR InterPro; IPR036020; WW_dom_sf.
DR PANTHER; PTHR11864; PTHR11864; 1.
DR Pfam; PF01846; FF; 3.
DR Pfam; PF00397; WW; 2.
DR SMART; SM00441; FF; 5.
DR SMART; SM00456; WW; 2.
DR SUPFAM; SSF51045; SSF51045; 2.
DR SUPFAM; SSF81698; SSF81698; 5.
DR PROSITE; PS51676; FF; 6.
DR PROSITE; PS50020; WW_DOMAIN_2; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; mRNA processing; mRNA splicing; Nucleus;
KW Phosphoprotein; Reference proteome; Repeat.
FT CHAIN 1..958
FT /note="Pre-mRNA-processing protein 40A"
FT /id="PRO_0000418357"
FT DOMAIN 184..217
FT /note="WW 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00224"
FT DOMAIN 225..258
FT /note="WW 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00224"
FT DOMAIN 404..458
FT /note="FF 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01013"
FT DOMAIN 471..526
FT /note="FF 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01013"
FT DOMAIN 532..593
FT /note="FF 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01013"
FT DOMAIN 611..674
FT /note="FF 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01013"
FT DOMAIN 679..734
FT /note="FF 5"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01013"
FT DOMAIN 736..801
FT /note="FF 6"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01013"
FT REGION 1..54
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 89..132
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 158..193
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 270..292
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 328..391
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 805..958
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..18
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 158..192
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 332..382
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 805..876
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 888..911
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 921..952
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 387
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT VAR_SEQ 923..926
FT /note="HANS -> VGTP (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_044036"
FT VAR_SEQ 927..958
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_044037"
SQ SEQUENCE 958 AA; 109382 MW; 3A59AB9520C49912 CRC64;
MANNPPQSSG TQFRPMVPGQ QGQHFVPAAS QPFHPYGHVP PNVQSQPPQY SQPIQQQQLF
PVRPGQPVHI TSSSQAVSVP YIQTNKILTS GSTQPQPNAP PMTGFATSGP PFSSPYTFVP
SSYPQQQPTS LVQPNSQMHV AGVPPAANTW PVPVNQSTSL VSPVQQTGQQ TPVAVSTDPG
NLTPQSASDW QEHTSADGRK YYYNKRTKQS NWEKPLELMT PLERADASTV WKEFTTPEGK
KYYYNKVTKE SKWTIPEDLK LAREQAQLAS EKTSLSEAGS TPLSHHAASS SDLAVSTVTS
VVPSTSSALT GHSSSPIQAG LAVPVTRPPS VAPVTPTSGA ISDTEATTIK GDNLSSRGAD
DSNDGATAQN NEAENKEMSV NGKANLSPAG DKANVEEPMV YATKQEAKAA FKSLLESVNV
HSDWTWEQTL KEIVHDKRYG ALRTLGERKQ AFNEYLGQRK KVEAEERRRR QKKAREEFVK
MLEECEELSS SLKWSKAMSL FENDQRFKAV DRPRDREDLF DNYIVELERK EREKAAEEHR
QYMADYRKFL ETCDYIKAGT QWRKIQDRLE DDDRCSCLEK IDRLIGFEEY ILDLEKEEEE
LKRVEKEHVR RAERKNRDAF RTLLEEHVAA GILTAKTYWL DYCIELKDLP QYQAVASNTS
GSTPKDLFED VTEELEKQYH EDKSYVKDAM KSRKISMVSS WLFEDFKSAI SEDLSTQQIS
DINLKLIYDD LVGRVKEKEE KEARKLQRLA EEFTNLLHTF KEITVASNWE DSKQLVEESQ
EYRSIGDESV SQGLFEEYIT SLQEKAKEKE RKRDEEKVRK EKERDEKEKR KDKDKERREK
EREREKEKGK ERSKREESDG ETAMDVSEGH KDEKRKGKDR DRKHRRRHHN NSDEDVSSDR
DDRDESKKSS RKHGNDRKKS RKHANSPESE SENRHKRQKK ESSRRSGNDE LEDGEVGE
