RUB1_ARATH
ID RUB1_ARATH Reviewed; 156 AA.
AC Q9SHE7; O80715; P59263; Q0WQU3; Q38875; Q9LDJ2; Q9LYW1; Q9M0W3; Q9M1P9;
AC Q9S7X3;
DT 31-OCT-2003, integrated into UniProtKB/Swiss-Prot.
DT 10-AUG-2010, sequence version 3.
DT 25-MAY-2022, entry version 144.
DE RecName: Full=Ubiquitin-NEDD8-like protein RUB1;
DE Contains:
DE RecName: Full=Ubiquitin;
DE Contains:
DE RecName: Full=NEDD8-like protein RUB1;
DE AltName: Full=Ubiquitin-related protein 1;
DE Short=AtRUB1;
DE Flags: Precursor;
GN Name=RUB1; Synonyms=NEDD8, UBQ15; OrderedLocusNames=At1g31340;
GN ORFNames=T19E23.13;
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, AND INTERACTION WITH AXR1 AND ECR1.
RX PubMed=9624055; DOI=10.1126/science.280.5370.1760;
RA del Pozo J.C., Timpte C., Tan S., Callis J., Estelle M.;
RT "The ubiquitin-related protein RUB1 and auxin response in Arabidopsis.";
RL Science 280:1760-1763(1998).
RN [6]
RP FUNCTION.
RX PubMed=10611386; DOI=10.1073/pnas.96.26.15342;
RA del Pozo J.C., Estelle M.;
RT "The Arabidopsis cullin AtCUL1 is modified by the ubiquitin-related protein
RT RUB1.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:15342-15347(1999).
RN [7]
RP INTERACTION WITH ML3.
RX PubMed=23903439; DOI=10.1104/pp.113.221341;
RA Hakenjos J.P., Bejai S., Ranftl Q., Behringer C., Vlot A.C., Absmanner B.,
RA Hammes U., Heinzlmeir S., Kuster B., Schwechheimer C.;
RT "ML3 is a NEDD8- and ubiquitin-modified protein.";
RL Plant Physiol. 163:135-149(2013).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 79-152, AND TISSUE SPECIFICITY.
RX PubMed=9857029; DOI=10.1074/jbc.273.52.34976;
RA Rao-Naik C., delaCruz W., Laplaza J.M., Tan S., Callis J., Fisher A.J.;
RT "The rub family of ubiquitin-like proteins. Crystal structure of
RT Arabidopsis rub1 and expression of multiple rubs in Arabidopsis.";
RL J. Biol. Chem. 273:34976-34982(1998).
CC -!- FUNCTION: Ubiquitin exists either covalently attached to another
CC protein, or free (unanchored). When covalently bound, it is conjugated
CC to target proteins via an isopeptide bond either as a monomer
CC (monoubiquitin), a polymer linked via different Lys residues of the
CC ubiquitin (polyubiquitin chains) or a linear polymer linked via the
CC initiator Met of the ubiquitin (linear polyubiquitin chains).
CC Polyubiquitin chains, when attached to a target protein, have different
CC functions depending on the Lys residue of the ubiquitin that is linked:
CC Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated
CC degradation) and in cell-cycle regulation; Lys-29-linked is involved in
CC lysosomal degradation; Lys-33-linked is involved in kinase
CC modification; Lys-48-linked is involved in protein degradation via the
CC proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage
CC responses. Linear polymer chains formed via attachment by the initiator
CC Met lead to cell signaling. Ubiquitin is usually conjugated to Lys
CC residues of target proteins, however, in rare cases, conjugation to Cys
CC or Ser residues has been observed. When polyubiquitin is free
CC (unanchored-polyubiquitin), it also has distinct roles, such as in
CC activation of protein kinases, and in signaling (By similarity).
CC {ECO:0000250}.
CC -!- FUNCTION: [NEDD8-like protein RUB1]: Appears to function as a stable
CC post-translational protein modifier. An AMP-RUB1 intermediate is formed
CC by an activating enzyme, distinct from the ubiquitin activating enzyme
CC E1, which is composed of a heterodimer AXR1/ECR1. Auxin response is
CC mediated, at least in part, through modification of the cullin AtCUL1
CC by the attachment of RUB1 to 'Lys-692'. {ECO:0000269|PubMed:10611386,
CC ECO:0000269|PubMed:9624055}.
CC -!- SUBUNIT: [NEDD8-like protein RUB1]: Forms a thiol ester with the
CC heterodimer AXR1/ECR1, specifically with the 'Cys-215' of ECR1
CC (PubMed:9624055). Interacts with ML3 (PubMed:23903439).
CC {ECO:0000269|PubMed:23903439, ECO:0000269|PubMed:9624055}.
CC -!- SUBCELLULAR LOCATION: [Ubiquitin]: Cytoplasm {ECO:0000250}. Nucleus
CC {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves, stems and flowers.
CC {ECO:0000269|PubMed:9857029}.
CC -!- MISCELLANEOUS: Ubiquitin is encoded by 16 different genes. Ubiquitin is
CC generally synthesized as a polyubiquitin precursor with tandem head to
CC tail repeats. Often, there is one to three additional amino acids after
CC the last repeat, removed in the mature protein. Alternatively,
CC ubiquitin extension protein is synthesized as a single copy of
CC ubiquitin fused to a ribosomal protein (either L40 or S27A) or to a
CC ubiquitin-related protein (either RUB1 or RUB2). Following translation,
CC extension protein is cleaved from ubiquitin.
CC -!- SIMILARITY: Belongs to the ubiquitin family. {ECO:0000305}.
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DR EMBL; AC007654; AAF24594.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31344.1; -; Genomic_DNA.
DR EMBL; BT005749; AAO64156.1; -; mRNA.
DR EMBL; BT006110; AAP04095.1; -; mRNA.
DR EMBL; AK228591; BAF00506.1; -; mRNA.
DR PIR; C86439; C86439.
DR RefSeq; NP_564379.2; NM_102873.5.
DR PDB; 1BT0; X-ray; 1.70 A; A=77-152.
DR PDBsum; 1BT0; -.
DR AlphaFoldDB; Q9SHE7; -.
DR SMR; Q9SHE7; -.
DR BioGRID; 25258; 4.
DR STRING; 3702.AT1G31340.1; -.
DR PaxDb; Q9SHE7; -.
DR ProteomicsDB; 226614; -.
DR EnsemblPlants; AT1G31340.1; AT1G31340.1; AT1G31340.
DR GeneID; 840023; -.
DR Gramene; AT1G31340.1; AT1G31340.1; AT1G31340.
DR KEGG; ath:AT1G31340; -.
DR Araport; AT1G31340; -.
DR TAIR; locus:2197525; AT1G31340.
DR eggNOG; KOG0001; Eukaryota.
DR HOGENOM; CLU_010412_0_0_1; -.
DR InParanoid; Q9SHE7; -.
DR OMA; ETQIVTC; -.
DR OrthoDB; 1536766at2759; -.
DR PhylomeDB; Q9SHE7; -.
DR EvolutionaryTrace; Q9SHE7; -.
DR PRO; PR:Q9SHE7; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9SHE7; baseline and differential.
DR Genevisible; Q9SHE7; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0031386; F:protein tag; IBA:GO_Central.
DR GO; GO:0031625; F:ubiquitin protein ligase binding; IBA:GO_Central.
DR GO; GO:0009693; P:ethylene biosynthetic process; IMP:TAIR.
DR GO; GO:0019941; P:modification-dependent protein catabolic process; IBA:GO_Central.
DR GO; GO:0045116; P:protein neddylation; TAS:TAIR.
DR GO; GO:0016567; P:protein ubiquitination; IBA:GO_Central.
DR GO; GO:0009733; P:response to auxin; TAS:TAIR.
DR CDD; cd01806; Ubl_NEDD8; 1.
DR InterPro; IPR038738; Nedd8-like.
DR InterPro; IPR000626; Ubiquitin-like_dom.
DR InterPro; IPR029071; Ubiquitin-like_domsf.
DR InterPro; IPR019954; Ubiquitin_CS.
DR InterPro; IPR019956; Ubiquitin_dom.
DR Pfam; PF00240; ubiquitin; 2.
DR PRINTS; PR00348; UBIQUITIN.
DR SMART; SM00213; UBQ; 2.
DR SUPFAM; SSF54236; SSF54236; 2.
DR PROSITE; PS00299; UBIQUITIN_1; 2.
DR PROSITE; PS50053; UBIQUITIN_2; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Isopeptide bond; Nucleus; Reference proteome;
KW Repeat; Ubl conjugation pathway.
FT CHAIN 1..76
FT /note="Ubiquitin"
FT /id="PRO_0000396910"
FT CHAIN 77..152
FT /note="NEDD8-like protein RUB1"
FT /id="PRO_0000035965"
FT PROPEP 153..156
FT /evidence="ECO:0000305"
FT /id="PRO_0000035966"
FT DOMAIN 1..76
FT /note="Ubiquitin-like 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT DOMAIN 77..152
FT /note="Ubiquitin-like 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT CROSSLNK 76
FT /note="Glycyl lysine isopeptide (Gly-Lys) (interchain with
FT K-? in acceptor proteins)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT CROSSLNK 152
FT /note="Glycyl lysine isopeptide (Gly-Lys) (interchain with
FT K-? in acceptor proteins)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT STRAND 78..82
FT /evidence="ECO:0007829|PDB:1BT0"
FT STRAND 88..92
FT /evidence="ECO:0007829|PDB:1BT0"
FT HELIX 99..110
FT /evidence="ECO:0007829|PDB:1BT0"
FT HELIX 114..116
FT /evidence="ECO:0007829|PDB:1BT0"
FT STRAND 117..121
FT /evidence="ECO:0007829|PDB:1BT0"
FT HELIX 133..135
FT /evidence="ECO:0007829|PDB:1BT0"
FT STRAND 142..147
FT /evidence="ECO:0007829|PDB:1BT0"
SQ SEQUENCE 156 AA; 17397 MW; FA8D702BB9C1B3AE CRC64;
MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLADYN
IQKESTLHLV LRLRGGTMIK VKTLTGKEIE IDIEPTDTID RIKERVEEKE GIPPVQQRLI
YAGKQLADDK TAKDYNIEGG SVLHLVLALR GGFGLL
