RD23D_ARATH
ID RD23D_ARATH Reviewed; 378 AA.
AC Q84L30; Q94C35; Q9FF16;
DT 23-NOV-2004, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 2.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=Ubiquitin receptor RAD23d;
DE Short=AtRAD23d;
DE AltName: Full=Putative DNA repair protein RAD23-4;
DE AltName: Full=RAD23-like protein 4;
DE Short=AtRAD23-4;
GN Name=RAD23D; Synonyms=RAD23, RAD23-4; OrderedLocusNames=At5g38470;
GN ORFNames=MXI10.20;
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 [MRNA] (ISOFORMS 1 AND 2).
RC STRAIN=cv. Columbia; TISSUE=Flower bud;
RA Ishikawa Y., Endo M., Abe K., Osakabe K., Nakajima N., Saji H., Ito Y.,
RA Ichikawa H., Kameya T., Toki S.;
RT "Isolation of four RAD23 genes from Arabidopsis thaliana and detection of
RT alternative splicing variants.";
RL Submitted (APR-2003) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9330910; DOI=10.1093/dnares/4.3.215;
RA Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M.,
RA Miyajima N., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence
RT features of the 1.6 Mb regions covered by twenty physically assigned P1
RT clones.";
RL DNA Res. 4:215-230(1997).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 [6]
RP FUNCTION, AND INTERACTION WITH RPN10.
RX PubMed=20059542; DOI=10.1111/j.1742-4658.2009.07531.x;
RA Fatimababy A.S., Lin Y.L., Usharani R., Radjacommare R., Wang H.T.,
RA Tsai H.L., Lee Y., Fu H.;
RT "Cross-species divergence of the major recognition pathways of
RT ubiquitylated substrates for ubiquitin/26S proteasome-mediated
RT proteolysis.";
RL FEBS J. 277:796-816(2010).
RN [7]
RP GENE FAMILY, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, POLYUBIQUITIN
RP BINDING, AND DISRUPTION PHENOTYPE.
RX PubMed=20086187; DOI=10.1105/tpc.109.072660;
RA Farmer L.M., Book A.J., Lee K.H., Lin Y.L., Fu H., Vierstra R.D.;
RT "The RAD23 family provides an essential connection between the 26S
RT proteasome and ubiquitylated proteins in Arabidopsis.";
RL Plant Cell 22:124-142(2010).
RN [8]
RP REVIEW.
RX PubMed=20399133; DOI=10.1016/j.tplants.2010.03.004;
RA Fu H., Lin Y.L., Fatimababy A.S.;
RT "Proteasomal recognition of ubiquitylated substrates.";
RL Trends Plant Sci. 15:375-386(2010).
RN [9]
RP INTERACTION WITH RPN10, AND MUTAGENESIS OF LEU-8 AND ILE-46.
RX PubMed=21764993; DOI=10.1105/tpc.111.086702;
RA Lin Y.-L., Sung S.-C., Tsai H.-L., Yu T.-T., Radjacommare R., Usharani R.,
RA Fatimababy A.S., Lin H.-Y., Wang Y.-Y., Fu H.;
RT "The defective proteasome but not substrate recognition function is
RT responsible for the null phenotypes of the Arabidopsis proteasome subunit
RT RPN10.";
RL Plant Cell 23:2754-2773(2011).
CC -!- FUNCTION: May be involved in nucleotide excision repair (By
CC similarity). Binds and presumably selects ubiquitin-conjugates for
CC destruction. Prefers multiubiquitin chains rather than single
CC ubiquitins, with a binding affinity for 'Lys-48'-linked ubiquitin
CC chains. Acts as a ubiquitin receptor that associates with the 26S
CC proteasomal docking subunit RPN10 for the indirect recognition of
CC ubiquitinated substrates of ubiquitin/26S proteasome-mediated
CC proteolysis (UPP) (By similarity). {ECO:0000250,
CC ECO:0000269|PubMed:20059542}.
CC -!- SUBUNIT: Interacts with 'Lys-48'-linked polyubiquitin chains. Interacts
CC with RPN10 via its ubiquitin-like domain. {ECO:0000269|PubMed:20059542,
CC ECO:0000269|PubMed:21764993}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20086187}. Cytoplasm
CC {ECO:0000269|PubMed:20086187}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1; Synonyms=alpha;
CC IsoId=Q84L30-1; Sequence=Displayed;
CC Name=2; Synonyms=beta;
CC IsoId=Q84L30-2; Sequence=VSP_011877;
CC -!- TISSUE SPECIFICITY: Widely expressed in the whole plant.
CC {ECO:0000269|PubMed:20086187}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype.
CC {ECO:0000269|PubMed:20086187}.
CC -!- SIMILARITY: Belongs to the RAD23 family. {ECO:0000305}.
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DR EMBL; AB109198; BAC76394.1; -; mRNA.
DR EMBL; AB109199; BAC76395.1; -; mRNA.
DR EMBL; AB005248; BAB09359.1; -; Genomic_DNA.
DR EMBL; CP002688; AED94321.1; -; Genomic_DNA.
DR EMBL; AY037181; AAK59766.1; -; mRNA.
DR EMBL; AY058196; AAL25609.1; -; mRNA.
DR EMBL; AY081835; AAL87405.1; -; mRNA.
DR EMBL; AY087564; AAM65106.1; -; mRNA.
DR RefSeq; NP_198663.1; NM_123208.2. [Q84L30-1]
DR AlphaFoldDB; Q84L30; -.
DR SMR; Q84L30; -.
DR BioGRID; 19086; 5.
DR DIP; DIP-57201N; -.
DR IntAct; Q84L30; 4.
DR MINT; Q84L30; -.
DR STRING; 3702.AT5G38470.1; -.
DR TCDB; 3.A.16.1.5; the endoplasmic reticular retrotranslocon (er-rt) family.
DR iPTMnet; Q84L30; -.
DR PaxDb; Q84L30; -.
DR PRIDE; Q84L30; -.
DR ProteomicsDB; 225961; -. [Q84L30-1]
DR EnsemblPlants; AT5G38470.1; AT5G38470.1; AT5G38470. [Q84L30-1]
DR GeneID; 833835; -.
DR Gramene; AT5G38470.1; AT5G38470.1; AT5G38470. [Q84L30-1]
DR KEGG; ath:AT5G38470; -.
DR Araport; AT5G38470; -.
DR TAIR; locus:2177376; AT5G38470.
DR eggNOG; KOG0011; Eukaryota.
DR HOGENOM; CLU_040364_1_0_1; -.
DR InParanoid; Q84L30; -.
DR OMA; ANPLDIF; -.
DR OrthoDB; 1260050at2759; -.
DR PhylomeDB; Q84L30; -.
DR PRO; PR:Q84L30; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q84L30; baseline and differential.
DR Genevisible; Q84L30; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005654; C:nucleoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0003684; F:damaged DNA binding; IEA:InterPro.
DR GO; GO:0031593; F:polyubiquitin modification-dependent protein binding; IDA:UniProtKB.
DR GO; GO:0070628; F:proteasome binding; IDA:TAIR.
DR GO; GO:0043130; F:ubiquitin binding; IDA:TAIR.
DR GO; GO:0006289; P:nucleotide-excision repair; IEA:InterPro.
DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IBA:GO_Central.
DR GO; GO:0009409; P:response to cold; IEP:TAIR.
DR Gene3D; 1.10.10.540; -; 1.
DR InterPro; IPR004806; Rad23.
DR InterPro; IPR006636; STI1_HS-bd.
DR InterPro; IPR015940; UBA.
DR InterPro; IPR009060; UBA-like_sf.
DR InterPro; IPR000626; Ubiquitin-like_dom.
DR InterPro; IPR029071; Ubiquitin-like_domsf.
DR InterPro; IPR015360; XPC-bd.
DR InterPro; IPR036353; XPC-bd_sf.
DR Pfam; PF00627; UBA; 2.
DR Pfam; PF00240; ubiquitin; 1.
DR Pfam; PF09280; XPC-binding; 1.
DR PRINTS; PR01839; RAD23PROTEIN.
DR SMART; SM00727; STI1; 1.
DR SMART; SM00165; UBA; 2.
DR SMART; SM00213; UBQ; 1.
DR SUPFAM; SSF101238; SSF101238; 1.
DR SUPFAM; SSF46934; SSF46934; 2.
DR SUPFAM; SSF54236; SSF54236; 1.
DR TIGRFAMs; TIGR00601; rad23; 1.
DR PROSITE; PS50030; UBA; 2.
DR PROSITE; PS50053; UBIQUITIN_2; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cytoplasm; DNA damage; DNA repair; Nucleus;
KW Reference proteome; Repeat.
FT CHAIN 1..378
FT /note="Ubiquitin receptor RAD23d"
FT /id="PRO_0000114911"
FT DOMAIN 1..78
FT /note="Ubiquitin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT DOMAIN 146..189
FT /note="UBA 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT DOMAIN 251..294
FT /note="STI1"
FT DOMAIN 330..371
FT /note="UBA 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT REGION 80..118
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 203..239
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 282..316
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.1"
FT /id="VSP_011877"
FT MUTAGEN 8
FT /note="L->A: Abolishes interaction with RPN10."
FT /evidence="ECO:0000269|PubMed:21764993"
FT MUTAGEN 46
FT /note="I->A: Abolishes interaction with RPN10."
FT /evidence="ECO:0000269|PubMed:21764993"
FT CONFLICT 260
FT /note="Q -> H (in Ref. 4; AAK59766)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 378 AA; 40066 MW; DD9B59153EA3E6A9 CRC64;
MKIFVKTLSG SNFEIEVKPA DKVSDVKTAI ETVKGAEYPA AKQMLIHQGK VLKDETTLEE
NNVVENSFIV IMLSKTKASP SGASTASAPA PSATQPQTVA TPQVSAPTAS VPVPTSGTAT
AAAPATAASV QTDVYGQAAS NLVAGTTLES TVQQILDMGG GSWDRDTVVR ALRAAFNNPE
RAVEYLYSGI PAQAEIPPVA QAPATGEQAA NPLAQPQQAA APAAATGGPN ANPLNLFPQG
MPAADAGAGA GNLDFLRNSQ QFQALRAMVQ ANPQILQPML QELGKQNPQL VRLIQEHQAD
FLRLINEPVE GEENVMEQLE AAMPQAVTVT PEEREAIERL EGMGFDRAMV LEVFFACNKN
EELAANYLLD HMHEFEDQ
