PUB13_ARATH
ID PUB13_ARATH Reviewed; 660 AA.
AC Q9SNC6;
DT 26-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 25-MAY-2022, entry version 151.
DE RecName: Full=U-box domain-containing protein 13;
DE EC=2.3.2.27;
DE AltName: Full=Plant U-box protein 13;
DE AltName: Full=RING-type E3 ubiquitin transferase PUB13 {ECO:0000305};
GN Name=PUB13; OrderedLocusNames=At3g46510; ORFNames=F12A12.30;
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].
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 GENE FAMILY ORGANIZATION, AND NOMENCLATURE.
RX PubMed=11495788; DOI=10.1016/s1360-1385(01)01960-4;
RA Azevedo C., Santos-Rosa M.J., Shirasu K.;
RT "The U-box protein family in plants.";
RL Trends Plant Sci. 6:354-358(2001).
RN [5]
RP GENE FAMILY ORGANIZATION.
RX PubMed=14657406; DOI=10.1104/pp.103.029553;
RA Mudgil Y., Shiu S.-H., Stone S.L., Salt J.N., Goring D.R.;
RT "A large complement of the predicted Arabidopsis ARM repeat proteins are
RT members of the U-box E3 ubiquitin ligase family.";
RL Plant Physiol. 134:59-66(2004).
RN [6]
RP INTERACTION WITH SD11; SD16; SD17; SD18; SD113; SD129 AND SD25,
RP PHOSPHORYLATION, AND SUBCELLULAR LOCATION.
RX PubMed=18552232; DOI=10.1104/pp.108.123380;
RA Samuel M.A., Mudgil Y., Salt J.N., Delmas F., Ramachandran S., Chilelli A.,
RA Goring D.R.;
RT "Interactions between the S-domain receptor kinases and AtPUB-ARM E3
RT ubiquitin ligases suggest a conserved signaling pathway in Arabidopsis.";
RL Plant Physiol. 147:2084-2095(2008).
RN [7]
RP IDENTIFICATION BY 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).
CC -!- FUNCTION: Functions as an E3 ubiquitin ligase. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC EC=2.3.2.27;
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC -!- SUBUNIT: Binds to SD11, SD16, SD17, SD18, SD113, SD129 and SD25.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:18552232}. Cytoplasm
CC {ECO:0000269|PubMed:18552232}.
CC -!- PTM: Phosphorylated by SD1-6 and SD1-7. {ECO:0000269|PubMed:18552232}.
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DR EMBL; AL133314; CAB62321.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78167.1; -; Genomic_DNA.
DR EMBL; AY042791; AAK68731.1; -; mRNA.
DR EMBL; AY128813; AAM91213.1; -; mRNA.
DR PIR; T45588; T45588.
DR RefSeq; NP_190235.1; NM_114518.4.
DR AlphaFoldDB; Q9SNC6; -.
DR SMR; Q9SNC6; -.
DR BioGRID; 9124; 7.
DR STRING; 3702.AT3G46510.1; -.
DR iPTMnet; Q9SNC6; -.
DR PaxDb; Q9SNC6; -.
DR PRIDE; Q9SNC6; -.
DR ProteomicsDB; 224848; -.
DR EnsemblPlants; AT3G46510.1; AT3G46510.1; AT3G46510.
DR GeneID; 823804; -.
DR Gramene; AT3G46510.1; AT3G46510.1; AT3G46510.
DR KEGG; ath:AT3G46510; -.
DR Araport; AT3G46510; -.
DR TAIR; locus:2075140; AT3G46510.
DR eggNOG; KOG0167; Eukaryota.
DR HOGENOM; CLU_006348_5_1_1; -.
DR InParanoid; Q9SNC6; -.
DR OMA; VDDYQPT; -.
DR OrthoDB; 389393at2759; -.
DR PhylomeDB; Q9SNC6; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:Q9SNC6; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SNC6; baseline and differential.
DR Genevisible; Q9SNC6; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0070696; F:transmembrane receptor protein serine/threonine kinase binding; IPI:UniProtKB.
DR GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:TAIR.
DR GO; GO:0007166; P:cell surface receptor signaling pathway; IEA:InterPro.
DR GO; GO:0042742; P:defense response to bacterium; IGI:TAIR.
DR GO; GO:0043066; P:negative regulation of apoptotic process; IMP:CACAO.
DR GO; GO:0050777; P:negative regulation of immune response; IGI:TAIR.
DR GO; GO:0016567; P:protein ubiquitination; IDA:TAIR.
DR GO; GO:2000028; P:regulation of photoperiodism, flowering; IMP:CACAO.
DR CDD; cd16664; RING-Ubox_PUB; 1.
DR Gene3D; 1.20.930.20; -; 1.
DR Gene3D; 1.25.10.10; -; 2.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR036537; Adaptor_Cbl_N_dom_sf.
DR InterPro; IPR011989; ARM-like.
DR InterPro; IPR016024; ARM-type_fold.
DR InterPro; IPR000225; Armadillo.
DR InterPro; IPR045210; RING-Ubox_PUB.
DR InterPro; IPR003613; Ubox_domain.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF00514; Arm; 3.
DR Pfam; PF04564; U-box; 1.
DR SMART; SM00185; ARM; 6.
DR SMART; SM00504; Ubox; 1.
DR SUPFAM; SSF48371; SSF48371; 1.
DR PROSITE; PS50176; ARM_REPEAT; 2.
DR PROSITE; PS51698; U_BOX; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Nucleus; Phosphoprotein; Reference proteome; Repeat;
KW Transferase; Ubl conjugation pathway.
FT CHAIN 1..660
FT /note="U-box domain-containing protein 13"
FT /id="PRO_0000322158"
FT DOMAIN 255..329
FT /note="U-box"
FT REPEAT 384..423
FT /note="ARM 1"
FT REPEAT 425..464
FT /note="ARM 2"
FT REPEAT 466..505
FT /note="ARM 3"
FT REPEAT 507..546
FT /note="ARM 4"
FT REPEAT 548..587
FT /note="ARM 5"
FT REGION 227..252
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 631..660
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 235..252
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 631..654
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 660 AA; 71966 MW; 2742A7D472B73BD4 CRC64;
MEEEKASAAQ SLIDVVNEIA AISDYRITVK KLCYNLARRL KLLVPMFEEI RESNEPISED
TLKTLMNLKE AMCSAKDYLK FCSQGSKIYL VMEREQVTSK LMEVSVKLEQ SLSQIPYEEL
DISDEVREQV ELVLSQFRRA KGRVDVSDDE LYEDLQSLCN KSSDVDAYQP VLERVAKKLH
LMEIPDLAQE SVALHEMVAS SGGDVGENIE EMAMVLKMIK DFVQTEDDNG EEQKVGVNSR
SNGQTSTAAS QKIPVIPDDF RCPISLEMMR DPVIVSSGQT YERTCIEKWI EGGHSTCPKT
QQALTSTTLT PNYVLRSLIA QWCEANDIEP PKPPSSLRPR KVSSFSSPAE ANKIEDLMWR
LAYGNPEDQR SAAGEIRLLA KRNADNRVAI AEAGAIPLLV GLLSTPDSRI QEHSVTALLN
LSICENNKGA IVSAGAIPGI VQVLKKGSME ARENAAATLF SLSVIDENKV TIGALGAIPP
LVVLLNEGTQ RGKKDAATAL FNLCIYQGNK GKAIRAGVIP TLTRLLTEPG SGMVDEALAI
LAILSSHPEG KAIIGSSDAV PSLVEFIRTG SPRNRENAAA VLVHLCSGDP QHLVEAQKLG
LMGPLIDLAG NGTDRGKRKA AQLLERISRL AEQQKETAVS QPEEEAEPTH PESTTEAADT
