ID UBA3_ARATH Reviewed; 454 AA.
AC O65041; Q0WWG4; Q94A29;
DT 31-OCT-2003, integrated into UniProtKB/Swiss-Prot.
DT 12-JUN-2007, sequence version 2.
DT 24-JAN-2024, entry version 167.
DE RecName: Full=NEDD8-activating enzyme E1 catalytic subunit;
DE EC=6.2.1.64;
DE AltName: Full=RUB-activating enzyme;
DE AltName: Full=Ubiquitin-activating enzyme E1-like protein;
GN Name=ECR1; OrderedLocusNames=At5g19180; ORFNames=T24G5_80;
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], INTERACTION WITH AXR1 AND RUB1, MUTAGENESIS OF
RP CYS-215, AND FUNCTION.
RC STRAIN=cv. Columbia;
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 [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
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].
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].
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 [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 TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RX PubMed=11884684; DOI=10.1105/tpc.010282;
RA del Pozo J.C., Dharmasiri S., Hellmann H., Walker L., Gray W.M.,
RA Estelle M.;
RT "AXR1-ECR1-dependent conjugation of RUB1 to the Arabidopsis Cullin AtCUL1
RT is required for auxin response.";
RL Plant Cell 14:421-433(2002).
RN [8]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
CC -!- FUNCTION: Catalytic subunit of the dimeric ECR1-AXR1 E1 enzyme. E1
CC activates NEDD8/RUB1 by first adenylating its C-terminal glycine
CC residue with ATP, thereafter linking this residue to the side chain of
CC the catalytic cysteine, yielding a NEDD8-ECR1 thioester and free AMP.
CC E1 finally transfers NEDD8 to the catalytic cysteine of RCE1 (By
CC similarity). {ECO:0000250, ECO:0000269|PubMed:10611386,
CC ECO:0000269|PubMed:9624055}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-
CC cysteine = AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8
CC protein]-yl-L-cysteine.; EC=6.2.1.64;
CC -!- PATHWAY: Protein modification; protein neddylation.
CC -!- SUBUNIT: Heterodimer of UBA3/ECR1 and AXR1. Interacts with NEDD8 and
CC RCE1. {ECO:0000269|PubMed:9624055}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Expressed in shoot, root and floral meristems, in
CC vascular tissues of cotyledons and mature leaves, and in the stele of
CC the root. {ECO:0000269|PubMed:11884684}.
CC -!- DEVELOPMENTAL STAGE: Expressed during ovules and embryo development.
CC {ECO:0000269|PubMed:11884684}.
CC -!- INDUCTION: No accumulation in response to auxin treatment.
CC -!- MISCELLANEOUS: The formation of the adenylate intermediate is possible
CC in absence of AXR1 and without the participation of Cys-215.
CC -!- SIMILARITY: Belongs to the ubiquitin-activating E1 family. UBA3
CC subfamily. {ECO:0000305}.
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DR EMBL; AF051135; AAC27035.1; -; mRNA.
DR EMBL; AC069326; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002688; AED92667.1; -; Genomic_DNA.
DR EMBL; AY050426; AAK91442.1; -; mRNA.
DR EMBL; AY120692; AAM52235.1; -; mRNA.
DR EMBL; AK226388; BAE98534.1; -; mRNA.
DR PIR; T52253; T52253.
DR RefSeq; NP_568370.1; NM_121923.4.
DR AlphaFoldDB; O65041; -.
DR SMR; O65041; -.
DR BioGRID; 17314; 5.
DR STRING; 3702.O65041; -.
DR iPTMnet; O65041; -.
DR PaxDb; 3702-AT5G19180-1; -.
DR ProteomicsDB; 228599; -.
DR EnsemblPlants; AT5G19180.1; AT5G19180.1; AT5G19180.
DR GeneID; 832038; -.
DR Gramene; AT5G19180.1; AT5G19180.1; AT5G19180.
DR KEGG; ath:AT5G19180; -.
DR Araport; AT5G19180; -.
DR TAIR; AT5G19180; ECR1.
DR eggNOG; KOG2015; Eukaryota.
DR HOGENOM; CLU_013325_13_1_1; -.
DR InParanoid; O65041; -.
DR OMA; ATSCNPY; -.
DR OrthoDB; 20494at2759; -.
DR PhylomeDB; O65041; -.
DR UniPathway; UPA00885; -.
DR PRO; PR:O65041; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; O65041; baseline and differential.
DR Genevisible; O65041; AT.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0019781; F:NEDD8 activating enzyme activity; IDA:TAIR.
DR GO; GO:0046982; F:protein heterodimerization activity; NAS:TAIR.
DR GO; GO:0045116; P:protein neddylation; TAS:TAIR.
DR CDD; cd01488; Uba3_RUB; 1.
DR Gene3D; 3.40.50.720; NAD(P)-binding Rossmann-like Domain; 1.
DR Gene3D; 1.10.10.520; Ubiquitin activating enzymes (Uba3). Chain: B, domain 2; 1.
DR Gene3D; 3.10.290.20; Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3; 1.
DR InterPro; IPR014929; E2-binding.
DR InterPro; IPR045886; ThiF/MoeB/HesA.
DR InterPro; IPR000594; ThiF_NAD_FAD-bd.
DR InterPro; IPR023318; Ub_act_enz_dom_a_sf.
DR InterPro; IPR030468; Uba3_N.
DR InterPro; IPR035985; Ubiquitin-activating_enz.
DR InterPro; IPR033127; UBQ-activ_enz_E1_Cys_AS.
DR PANTHER; PTHR10953:SF6; NEDD8-ACTIVATING ENZYME E1 CATALYTIC SUBUNIT; 1.
DR PANTHER; PTHR10953; UBIQUITIN-ACTIVATING ENZYME E1; 1.
DR Pfam; PF08825; E2_bind; 1.
DR Pfam; PF00899; ThiF; 1.
DR SMART; SM01181; E2_bind; 1.
DR SUPFAM; SSF69572; Activating enzymes of the ubiquitin-like proteins; 1.
DR PROSITE; PS00865; UBIQUITIN_ACTIVAT_2; 1.
PE 1: Evidence at protein level;
KW Acetylation; ATP-binding; Ligase; Nucleotide-binding; Nucleus;
KW Reference proteome; Ubl conjugation pathway.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..454
FT /note="NEDD8-activating enzyme E1 catalytic subunit"
FT /id="PRO_0000194948"
FT ACT_SITE 215
FT /note="Glycyl thioester intermediate"
FT BINDING 56..80
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT MUTAGEN 215
FT /note="C->A: Loss of binding to RUB1."
FT /evidence="ECO:0000269|PubMed:9624055"
FT CONFLICT 189
FT /note="R -> K (in Ref. 1; AAC27035)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 454 AA; 50541 MW; 5B725F292DB3576A CRC64;
MADLDVPPQV PQSKTRDLDK LLLRHGNLVD PGFVPGPGLR DDIRDYVRIL VIGAGGLGCE
LLKDLALSGF RNLEVIDMDR IEVTNLNRQF LFRIEDVGKP KAEVAAKRVM ERVSGVEIVP
HFSRIEDKEI EFYNDFNIIA LGLDSIEARK YINGVACGFL EYNEDDTPKR ETIKPMVDGG
TEGFKGHARV ILPGVTPCFE CTIYLFPPQV KFPLCTLAET PRNAAHCIEY AHLIQWETVH
RGKTFDPDEP EHMKWVYDEA IRRAELFGIP GVTYSLTQGV VKNIIPAIAS TNAIISAACA
LETLKIVSAC SKTLVNYLTY NGGEGLYTEV TKFERDTECL VCGPGILIEL DTSVTLSKFI
EMLEDHPKLL LSKASVKQGE NTLYMQAPPV LEEFHRPKLS KPLYDLMGRV QKDTIHVFGQ
RALKNNEKES CTTKVRVVFK GADGVADMDT AIGA
//
