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Protein

Ubiquitin receptor RAD23c

Gene

RAD23C

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

May be involved in nucleotide excision repair (By similarity). Binds and presumably selects ubiquitin-conjugates for destruction. Prefers multiubiquitin chains rather than single ubiquitins, with a binding affinity for 'Lys-48'-linked ubiquitin chains. Acts as a ubiquitin receptor that associates with the 26S proteasomal docking subunit RPN10 for the indirect recognition of ubiquitinated substrates of ubiquitin/26S proteasome-mediated proteolysis (UPP).By similarity2 Publications

GO - Molecular functioni

  • damaged DNA binding Source: InterPro
  • polyubiquitin binding Source: UniProtKB
  • proteasome binding Source: TAIR
  • ubiquitin binding Source: TAIR

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA repair

Enzyme and pathway databases

ReactomeiR-ATH-5696394. DNA Damage Recognition in GG-NER.
R-ATH-5696395. Formation of Incision Complex in GG-NER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin receptor RAD23c
Short name:
AtRAD23c
Alternative name(s):
Putative DNA repair protein RAD23-3
RAD23-like protein 3
Short name:
AtRAD23-3
Gene namesi
Name:RAD23C
Synonyms:RAD23, RAD23-3
Ordered Locus Names:At3g02540
ORF Names:F16B3.17
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G02540.

Subcellular locationi

  • Nucleus 1 Publication
  • Cytoplasm 1 Publication

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

No visible phenotype.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi8 – 81L → A: Abolishes interaction with RPN10. 1 Publication
Mutagenesisi47 – 471I → A: Abolishes interaction with RPN10. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 419419Ubiquitin receptor RAD23cPRO_0000114910Add
BLAST

Proteomic databases

PaxDbiQ84L31.
PRIDEiQ84L31.

PTM databases

iPTMnetiQ84L31.

Expressioni

Tissue specificityi

Widely expressed in the whole plant.1 Publication

Gene expression databases

ExpressionAtlasiQ84L31. baseline and differential.
GenevisibleiQ84L31. AT.

Interactioni

Subunit structurei

Interacts with 'Lys-48'-linked polyubiquitin chains via its both UBA domains. Interacts with RPN10 via its ubiquitin-like domain.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
UBCP0CG482EBI-4437395,EBI-3390054From a different organism.

GO - Molecular functioni

  • polyubiquitin binding Source: UniProtKB
  • proteasome binding Source: TAIR
  • ubiquitin binding Source: TAIR

Protein-protein interaction databases

BioGridi6528. 3 interactions.
DIPiDIP-57199N.
IntActiQ84L31. 5 interactions.
MINTiMINT-7308028.
STRINGi3702.AT3G02540.1.

Structurei

3D structure databases

ProteinModelPortaliQ84L31.
SMRiQ84L31. Positions 1-413.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 7979Ubiquitin-likePROSITE-ProRule annotationAdd
BLAST
Domaini185 – 22844UBA 1PROSITE-ProRule annotationAdd
BLAST
Domaini288 – 33144STI1Add
BLAST
Domaini372 – 41342UBA 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi98 – 16669Pro-richAdd
BLAST

Sequence similaritiesi

Belongs to the RAD23 family.Curated
Contains 1 STI1 domain.Curated
Contains 2 UBA domains.PROSITE-ProRule annotation
Contains 1 ubiquitin-like domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0011. Eukaryota.
COG5272. LUCA.
HOGENOMiHOG000172162.
InParanoidiQ84L31.
KOiK10839.
OMAiNKNEEMA.
PhylomeDBiQ84L31.

Family and domain databases

Gene3Di1.10.10.540. 1 hit.
InterProiIPR004806. Rad23.
IPR006636. STI1_HS-bd.
IPR015940. UBA.
IPR009060. UBA-like.
IPR029071. Ubiquitin-rel_dom.
IPR000626. Ubiquitin_dom.
IPR015360. XPC-bd.
[Graphical view]
PfamiPF00627. UBA. 2 hits.
PF00240. ubiquitin. 1 hit.
PF09280. XPC-binding. 1 hit.
[Graphical view]
PRINTSiPR01839. RAD23PROTEIN.
SMARTiSM00727. STI1. 1 hit.
SM00165. UBA. 2 hits.
SM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF101238. SSF101238. 1 hit.
SSF46934. SSF46934. 2 hits.
SSF54236. SSF54236. 1 hit.
TIGRFAMsiTIGR00601. rad23. 1 hit.
PROSITEiPS50030. UBA. 2 hits.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q84L31-1) [UniParc]FASTAAdd to basket

Also known as: alpha

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MKIFVKTLKG THFEIEVKPE DSVVDVKKNI ESVQGADVYP AAKQMLIHQG
60 70 80 90 100
KVLKDETTIE ENKVAENSFI VIMMNKSKPA SAAASSASAG TSQAKSIPPS
110 120 130 140 150
TSQPSISPQT PASVSAPVAP APTRPPPPAP TPTPAPVAAT ETVTTPIPEP
160 170 180 190 200
VPATISSSTP APDSAPVGSQ GDVYGQAASN LAAGSNLEST IQQILDMGGG
210 220 230 240 250
TWDRETVVLA LRAAFNNPER AVEYLYTGIP EQAEVPPVAR PPASAGQPAN
260 270 280 290 300
PPAQTQQPAA APASGPNANP LDLFPQGLPN VGGNPGAGTL DFLRNSQQFQ
310 320 330 340 350
ALRAMVQANP QVLQPMLQEL GKQNPNLMRL IQDHQADFLR LINEPVEGGG
360 370 380 390 400
ESGNLLGQMA AGMPQPQAIQ VTHEEREAIE RLEAMGFERA LVLEVFFACN
410
KNEELAANYL LDHMHEFEE
Length:419
Mass (Da):44,247
Last modified:November 23, 2004 - v2
Checksum:iCAA13BC4FFEB1E25
GO
Isoform 2 (identifier: Q84L31-2) [UniParc]FASTAAdd to basket

Also known as: beta

The sequence of this isoform differs from the canonical sequence as follows:
     58-139: Missing.

Show »
Length:337
Mass (Da):36,221
Checksum:i6770375BB22527A5
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei58 – 13982Missing in isoform 2. 1 PublicationVSP_011876Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB109196 mRNA. Translation: BAC76392.1.
AB109197 mRNA. Translation: BAC76393.1.
AC021640 Genomic DNA. Translation: AAF32461.1.
CP002686 Genomic DNA. Translation: AEE73824.1.
AY039562 mRNA. Translation: AAK62617.1.
AY113034 mRNA. Translation: AAM47342.1.
RefSeqiNP_186903.1. NM_111121.3. [Q84L31-1]
UniGeneiAt.21477.

Genome annotation databases

EnsemblPlantsiAT3G02540.1; AT3G02540.1; AT3G02540. [Q84L31-1]
GeneIDi821195.
KEGGiath:AT3G02540.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB109196 mRNA. Translation: BAC76392.1.
AB109197 mRNA. Translation: BAC76393.1.
AC021640 Genomic DNA. Translation: AAF32461.1.
CP002686 Genomic DNA. Translation: AEE73824.1.
AY039562 mRNA. Translation: AAK62617.1.
AY113034 mRNA. Translation: AAM47342.1.
RefSeqiNP_186903.1. NM_111121.3. [Q84L31-1]
UniGeneiAt.21477.

3D structure databases

ProteinModelPortaliQ84L31.
SMRiQ84L31. Positions 1-413.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi6528. 3 interactions.
DIPiDIP-57199N.
IntActiQ84L31. 5 interactions.
MINTiMINT-7308028.
STRINGi3702.AT3G02540.1.

PTM databases

iPTMnetiQ84L31.

Proteomic databases

PaxDbiQ84L31.
PRIDEiQ84L31.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G02540.1; AT3G02540.1; AT3G02540. [Q84L31-1]
GeneIDi821195.
KEGGiath:AT3G02540.

Organism-specific databases

TAIRiAT3G02540.

Phylogenomic databases

eggNOGiKOG0011. Eukaryota.
COG5272. LUCA.
HOGENOMiHOG000172162.
InParanoidiQ84L31.
KOiK10839.
OMAiNKNEEMA.
PhylomeDBiQ84L31.

Enzyme and pathway databases

ReactomeiR-ATH-5696394. DNA Damage Recognition in GG-NER.
R-ATH-5696395. Formation of Incision Complex in GG-NER.

Miscellaneous databases

PROiQ84L31.

Gene expression databases

ExpressionAtlasiQ84L31. baseline and differential.
GenevisibleiQ84L31. AT.

Family and domain databases

Gene3Di1.10.10.540. 1 hit.
InterProiIPR004806. Rad23.
IPR006636. STI1_HS-bd.
IPR015940. UBA.
IPR009060. UBA-like.
IPR029071. Ubiquitin-rel_dom.
IPR000626. Ubiquitin_dom.
IPR015360. XPC-bd.
[Graphical view]
PfamiPF00627. UBA. 2 hits.
PF00240. ubiquitin. 1 hit.
PF09280. XPC-binding. 1 hit.
[Graphical view]
PRINTSiPR01839. RAD23PROTEIN.
SMARTiSM00727. STI1. 1 hit.
SM00165. UBA. 2 hits.
SM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF101238. SSF101238. 1 hit.
SSF46934. SSF46934. 2 hits.
SSF54236. SSF54236. 1 hit.
TIGRFAMsiTIGR00601. rad23. 1 hit.
PROSITEiPS50030. UBA. 2 hits.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation of four RAD23 genes from Arabidopsis thaliana and detection of alternative splicing variants."
    Ishikawa Y., Endo M., Abe K., Osakabe K., Nakajima N., Saji H., Ito Y., Ichikawa H., Kameya T., Toki S.
    Submitted (APR-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
    Strain: cv. Columbia.
    Tissue: Flower bud.
  2. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
    Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
    , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: cv. Columbia.
  5. "Cross-species divergence of the major recognition pathways of ubiquitylated substrates for ubiquitin/26S proteasome-mediated proteolysis."
    Fatimababy A.S., Lin Y.L., Usharani R., Radjacommare R., Wang H.T., Tsai H.L., Lee Y., Fu H.
    FEBS J. 277:796-816(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RPN10, POLYUBIQUITIN BINDING.
  6. "The RAD23 family provides an essential connection between the 26S proteasome and ubiquitylated proteins in Arabidopsis."
    Farmer L.M., Book A.J., Lee K.H., Lin Y.L., Fu H., Vierstra R.D.
    Plant Cell 22:124-142(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, POLYUBIQUITIN BINDING, DISRUPTION PHENOTYPE.
  7. "Proteasomal recognition of ubiquitylated substrates."
    Fu H., Lin Y.L., Fatimababy A.S.
    Trends Plant Sci. 15:375-386(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  8. "The defective proteasome but not substrate recognition function is responsible for the null phenotypes of the Arabidopsis proteasome subunit RPN10."
    Lin Y.L., Sung S.C., Tsai H.L., Yu T.T., Radjacommare R., Usharani R., Fatimababy A.S., Lin H.Y., Wang Y.Y., Fu H.
    Plant Cell 23:2754-2773(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, POLYUBIQUITIN BINDING, INTERACTION WITH RPN10, MUTAGENESIS OF LEU-8 AND ILE-47.

Entry informationi

Entry nameiRD23C_ARATH
AccessioniPrimary (citable) accession number: Q84L31
Secondary accession number(s): Q9M887
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 23, 2004
Last sequence update: November 23, 2004
Last modified: June 8, 2016
This is version 101 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.