PUM4_ARATH
ID PUM4_ARATH Reviewed; 1003 AA.
AC Q9SS47; Q8GY24;
DT 30-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT 30-NOV-2010, sequence version 2.
DT 03-AUG-2022, entry version 118.
DE RecName: Full=Pumilio homolog 4;
DE Short=APUM-4;
DE Short=AtPUM4;
GN Name=APUM4; OrderedLocusNames=At3g10360; ORFNames=F14P13.4;
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=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 [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 632-1003.
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 674-1003.
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 GENE FAMILY, FUNCTION, AND RNA-BINDING.
RX PubMed=19682068; DOI=10.1111/j.1742-4658.2009.07230.x;
RA Francischini C.W., Quaggio R.B.;
RT "Molecular characterization of Arabidopsis thaliana PUF proteins -- binding
RT specificity and target candidates.";
RL FEBS J. 276:5456-5470(2009).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-225, 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 GENE FAMILY.
RX PubMed=20214804; DOI=10.1186/1471-2229-10-44;
RA Tam P.P., Barrette-Ng I.H., Simon D.M., Tam M.W., Ang A.L., Muench D.G.;
RT "The Puf family of RNA-binding proteins in plants: phylogeny, structural
RT modeling, activity and subcellular localization.";
RL BMC Plant Biol. 10:44-44(2010).
CC -!- FUNCTION: Sequence-specific RNA-binding protein that regulates
CC translation and mRNA stability by binding the 3'-UTR of target mRNAs.
CC Binds the APUM-binding elements (APBEs) in the 3'-UTR mRNA sequence of
CC CLV1, PNH, WUS and FAS2. {ECO:0000269|PubMed:19682068}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DOMAIN: The pumilio repeats mediate the association with RNA by packing
CC together to form a right-handed superhelix that approximates a half
CC donut. The number as well as the specific sequence of the repeats
CC determine the specificity for target mRNAs (By similarity).
CC {ECO:0000250}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF02808.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAC42549.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AC009400; AAF02808.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE74896.1; -; Genomic_DNA.
DR EMBL; AK117911; BAC42549.1; ALT_INIT; mRNA.
DR EMBL; BT005311; AAO63375.1; -; mRNA.
DR RefSeq; NP_187647.2; NM_111871.7.
DR AlphaFoldDB; Q9SS47; -.
DR SMR; Q9SS47; -.
DR STRING; 3702.AT3G10360.1; -.
DR iPTMnet; Q9SS47; -.
DR PaxDb; Q9SS47; -.
DR PRIDE; Q9SS47; -.
DR ProteomicsDB; 226082; -.
DR EnsemblPlants; AT3G10360.1; AT3G10360.1; AT3G10360.
DR GeneID; 820198; -.
DR Gramene; AT3G10360.1; AT3G10360.1; AT3G10360.
DR KEGG; ath:AT3G10360; -.
DR Araport; AT3G10360; -.
DR TAIR; locus:2076324; AT3G10360.
DR eggNOG; KOG1488; Eukaryota.
DR HOGENOM; CLU_004017_1_0_1; -.
DR InParanoid; Q9SS47; -.
DR OMA; DGNIMKC; -.
DR OrthoDB; 151468at2759; -.
DR PhylomeDB; Q9SS47; -.
DR PRO; PR:Q9SS47; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SS47; baseline and differential.
DR Genevisible; Q9SS47; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0003729; F:mRNA binding; IDA:UniProtKB.
DR GO; GO:0010608; P:post-transcriptional regulation of gene expression; IBA:GO_Central.
DR GO; GO:0006417; P:regulation of translation; IEA:UniProtKB-KW.
DR CDD; cd07920; Pumilio; 1.
DR Gene3D; 1.25.10.10; -; 1.
DR InterPro; IPR011989; ARM-like.
DR InterPro; IPR016024; ARM-type_fold.
DR InterPro; IPR012940; NABP.
DR InterPro; IPR033133; PUM-HD.
DR InterPro; IPR033712; Pumilio_RNA-bd.
DR InterPro; IPR001313; Pumilio_RNA-bd_rpt.
DR Pfam; PF07990; NABP; 1.
DR Pfam; PF00806; PUF; 8.
DR SMART; SM00025; Pumilio; 8.
DR SUPFAM; SSF48371; SSF48371; 1.
DR PROSITE; PS50302; PUM; 9.
DR PROSITE; PS50303; PUM_HD; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Phosphoprotein; Reference proteome; Repeat; RNA-binding;
KW Translation regulation.
FT CHAIN 1..1003
FT /note="Pumilio homolog 4"
FT /id="PRO_0000401386"
FT DOMAIN 644..984
FT /note="PUM-HD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00318"
FT REPEAT 664..699
FT /note="Pumilio 1"
FT REPEAT 700..735
FT /note="Pumilio 2"
FT REPEAT 736..771
FT /note="Pumilio 3"
FT REPEAT 772..807
FT /note="Pumilio 4"
FT REPEAT 808..843
FT /note="Pumilio 5"
FT REPEAT 845..880
FT /note="Pumilio 6"
FT REPEAT 881..916
FT /note="Pumilio 7"
FT REPEAT 917..958
FT /note="Pumilio 8"
FT REGION 38..65
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 285..328
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 43..57
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 285..312
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 225
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT MOD_RES 305
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:Q9ZW02"
FT CONFLICT 687
FT /note="E -> K (in Ref. 3; BAC42549 and 4; AAO63375)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1003 AA; 111613 MW; C242B56F22A8BD3E CRC64;
MVTNSYMDTR SNLTSVNRGS NVDLEDRFQR ELESLLQQHR NQQSFGRERE RDIDVHRSGS
APPTVEGLLR AMDNQYLNNN NSDHRDVGNI SSITTSNGVE LLSDDELRWH PEYLSYYYSN
EHSNPRLPPP LLSREDWRVA QRFHNSESVF DPVGEWRKKT VEVDNSSSLF SVQPGVPVEQ
AENDLMELRN AVAQGRSQKV QRLDQGREDL IGLSGYSGLG PRRKSFADIL QEGLERDAAL
GSQLSRPASC NTFRDMKDAA VLSNFSAGGF DSPLAFHDSL HSTAKNSPNT MLGSTMSSPV
PRNRTPDSHL VGRSTASGLP PIGTRVGPVE KKNTFGTAIQ NCESYTAADV ADTLSRLNMS
EMSQVKENHM QSQLQVELEN QSDVMRYIPN GHKKALRQQN TAETKDHLFS ANYGGMSGYG
ASLGASTVGS HGQVNIPKRT SSSASLYSTS DHSRLGSVGL SDVNIRNGNI NGTDFSTAGG
YMAKNKLNSL AEHYSAEGSH LTGDGDRQSL NRLINQVASE LHSPVMDPHY SQYLHTASST
AAPIDHSLIR NNFGTSNGDT ANEYLAMLLA QNRQQLGNLN AANSRFFESP SYDLGNMYLG
NHLPSPSKNS RNFQNMRMSQ SASMMKVPFG GLQGSSHVDI GSTAEASLLE GFKNNKTRSL
ELSEIVGHVI EFSMDQYGSR FIQQKLETAT DEEKNAIFPE ILPYGRTLMT DVFGNYVIQK
FFEHGTTKQR KELAEQVTGH VLALSLQMYG CRVIQKALEV VELEQQARMV KELDGSVMKC
VHDQNGNHVI QKCIERLPQD WIQFIISSFY GKVLALSTHP YGCRVIQRVL EHIDDIETQR
IIMEEIMDSV CTLAQDQYGN YVIQHIIQHG KPHERSEIIN KLAGQIVKMS QQKFASNVVE
KCLTFGGPEE RQVLVNEMLG YTDENEPLQA MMKDPFGNYV VQKVLETCDD QSLALILSRI
KVHLNALKRY TYGKHIVARV EKLITTGERR IGLSSSLAAN TTP
