PR40B_ARATH
ID PR40B_ARATH Reviewed; 992 AA.
AC F4JCC1; A0A1I9LM86; Q9LJM8;
DT 11-JUL-2012, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 25-MAY-2022, entry version 73.
DE RecName: Full=Pre-mRNA-processing protein 40B;
DE Short=AtPRP40b {ECO:0000303|PubMed:19467629};
GN Name=PRP40B {ECO:0000303|PubMed:19467629};
GN Synonyms=MED35_2 {ECO:0000303|PubMed:22021418}, MED35B;
GN OrderedLocusNames=At3g19670 {ECO:0000312|Araport:AT3G19670};
GN ORFNames=MMB12.15 {ECO:0000312|EMBL:BAB02553.1};
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=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(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 IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=17272265; DOI=10.1074/mcp.m600408-mcp200;
RA Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
RT "Multidimensional protein identification technology (MudPIT) analysis of
RT ubiquitinated proteins in plants.";
RL Mol. Cell. Proteomics 6:601-610(2007).
RN [4]
RP FUNCTION, INTERACTION WITH NRPB1, MUTAGENESIS OF TRP-209; ASP-216; TRP-231;
RP MET-238; TRP-250 AND TRP-272, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, AND
RP DISRUPTION 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 [5]
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 (PubMed:10907853). May be involved in pre-
CC mRNA splicing (Probable). {ECO:0000269|PubMed:10907853,
CC 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:0000269|PubMed:19467629}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, shoots, rosette leaves, cauline
CC leaves, stems and flowers. {ECO:0000269|PubMed:19467629}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions, probably due to the redundancy with PPRP40A and PPRP40C.
CC {ECO:0000269|PubMed:19467629}.
CC -!- SIMILARITY: Belongs to the PRPF40 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB02553.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP000417; BAB02553.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE76274.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM63694.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM63696.1; -; Genomic_DNA.
DR PIR; T52396; T52396.
DR RefSeq; NP_001325767.1; NM_001338414.1.
DR RefSeq; NP_001325769.1; NM_001338415.1.
DR RefSeq; NP_188601.4; NM_112857.6.
DR AlphaFoldDB; F4JCC1; -.
DR SMR; F4JCC1; -.
DR BioGRID; 6837; 2.
DR IntAct; F4JCC1; 1.
DR STRING; 3702.AT3G19670.1; -.
DR iPTMnet; F4JCC1; -.
DR PaxDb; F4JCC1; -.
DR PRIDE; F4JCC1; -.
DR ProteomicsDB; 225988; -.
DR EnsemblPlants; AT3G19670.1; AT3G19670.1; AT3G19670.
DR EnsemblPlants; AT3G19670.2; AT3G19670.2; AT3G19670.
DR EnsemblPlants; AT3G19670.3; AT3G19670.3; AT3G19670.
DR GeneID; 821504; -.
DR Gramene; AT3G19670.1; AT3G19670.1; AT3G19670.
DR Gramene; AT3G19670.2; AT3G19670.2; AT3G19670.
DR Gramene; AT3G19670.3; AT3G19670.3; AT3G19670.
DR KEGG; ath:AT3G19670; -.
DR Araport; AT3G19670; -.
DR TAIR; locus:2091171; AT3G19670.
DR eggNOG; KOG0152; Eukaryota.
DR HOGENOM; CLU_005825_2_0_1; -.
DR InParanoid; F4JCC1; -.
DR OrthoDB; 1112854at2759; -.
DR PRO; PR:F4JCC1; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; F4JCC1; baseline and differential.
DR Genevisible; F4JCC1; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
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; 4.
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; PS01159; WW_DOMAIN_1; 2.
DR PROSITE; PS50020; WW_DOMAIN_2; 2.
PE 1: Evidence at protein level;
KW Coiled coil; mRNA processing; mRNA splicing; Nucleus; Reference proteome;
KW Repeat.
FT CHAIN 1..992
FT /note="Pre-mRNA-processing protein 40B"
FT /id="PRO_0000418358"
FT DOMAIN 203..236
FT /note="WW 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00224"
FT DOMAIN 244..277
FT /note="WW 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00224"
FT DOMAIN 450..504
FT /note="FF 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01013"
FT DOMAIN 517..572
FT /note="FF 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01013"
FT DOMAIN 585..639
FT /note="FF 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01013"
FT DOMAIN 642..720
FT /note="FF 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01013"
FT DOMAIN 724..780
FT /note="FF 5"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01013"
FT DOMAIN 782..847
FT /note="FF 6"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01013"
FT REGION 1..22
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 307..329
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 361..442
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 855..992
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 958..986
FT /evidence="ECO:0000255"
FT COMPBIAS 1..18
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 361..384
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 399..421
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 423..439
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 855..914
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 922..943
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 953..992
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 209
FT /note="W->A: Loss of CTD binding."
FT /evidence="ECO:0000269|PubMed:19467629"
FT MUTAGEN 216
FT /note="D->A: No effect on CTD binding."
FT /evidence="ECO:0000269|PubMed:19467629"
FT MUTAGEN 231
FT /note="W->A: Decreased binding to CTD."
FT /evidence="ECO:0000269|PubMed:19467629"
FT MUTAGEN 238
FT /note="M->A: Moderate decrease of CTD binding."
FT /evidence="ECO:0000269|PubMed:19467629"
FT MUTAGEN 250
FT /note="W->A: Decreased binding to CTD."
FT /evidence="ECO:0000269|PubMed:19467629"
FT MUTAGEN 272
FT /note="W->A: Strong decrease of CTD binding."
FT /evidence="ECO:0000269|PubMed:19467629"
SQ SEQUENCE 992 AA; 113569 MW; 7061088BF30A7443 CRC64;
MANNHQYPGI QPFQHPNASS IDLPRGFAPP MNFQFLPTIQ APQSEQVARL SSQNFQCVGR
GGTVLSIGYP PQSYAPQLLQ SMHHSHERPS QLNQVQVQHV PLGPPTLISQ PNVSIASGTS
LHQPYVQTPD IGMPGFGGPR ALFSYPSATS YEGSRVPPQV TGPSIHSQAQ QRASIIHTSA
ESSIMNPTFE QPKAAFLKPL PSQKALTDWV EHTSADGRKY FFNKRTKKST WEKPVELMTL
FERADARTDW KEHSSPDGRK YYYNKITKQS TWTMPEEMKI VREQAEIASV QGPHAEGIID
ASEVLTRSDT ASTAAPTGLP SQTSTSEGVE KLTLTSDLKQ PASVPGSSSP VENVDRVQMS
ADETSQLCDT SETDGLSVPV TETSAATLVE KDEISVGNSG DSDDMSTKNA NQGSGSGPKE
SQKPMVESEK VESQTEEKQI HQESFSFNNK LEAVDVFKSL LKSAKVGSDW TWEQAMREII
NDKRYGALRT LGERKQAFNE FLLQTKRAAE EERLARQKKL YEDFKRMLEE CVELTPSTRW
SKTVTMFEDD ERFKALEREK DRRNIFEDHV SELKEKGRVK ALEDRKRNII EYKRFLESCN
FIKPNSQWRK VQDRLEVDER CSRLEKIDQL EIFQEYLRDL EREEEEKKKI QKEELKKVER
KHRDEFHGLL DEHIATGELT AKTIWRDYLM KVKDLPVYSA IASNSSGATP KDLFEDAVED
LKKRDHELKS QIKDVLKLRK VNLSAGSTFD EFKVSISEDI GFPLIPDVRL KLVFDDLLER
AKEKEEKEAR KQTRQTEKLV DMLRSFKDIT ASSSWEELKH LVEGSEKCST IGDESFRKRC
FEDYVSLLKE QSNRIKQNKK VPEDVREEHD KGRDKYGREK DRVRERDSDD HHKKGAAGKY
NHDMNEPHGK ERRRSGRDSH NRHRERHTSV KENDTDHFKE SHKAGGGHKK SRHQRGWVSE
AEVEGKEKRR RKEEAREHTK EEELEDGECG RY
