UBP6_ARATH
ID UBP6_ARATH Reviewed; 482 AA.
AC Q949Y0; Q56ZE7; Q9C8H9; Q9FPT4;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 6;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 6;
DE Short=AtUBP6;
DE AltName: Full=Ubiquitin thioesterase 6;
DE AltName: Full=Ubiquitin-specific-processing protease 6;
GN Name=UBP6; OrderedLocusNames=At1g51710; ORFNames=F19C24.8;
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], GENE FAMILY ORGANIZATION, AND NOMENCLATURE.
RC STRAIN=cv. Columbia;
RX PubMed=11115897; DOI=10.1104/pp.124.4.1828;
RA Yan N., Doelling J.H., Falbel T.G., Durski A.M., Vierstra R.D.;
RT "The ubiquitin-specific protease family from Arabidopsis. AtUBP1 and 2 are
RT required for the resistance to the amino acid analog canavanine.";
RL Plant Physiol. 124:1828-1843(2000).
RN [2]
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 [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].
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 336-482.
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 (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP INTERACTION WITH CALMODULIN, AND MUTAGENESIS OF CYS-113; TRP-175 AND
RP LEU-178.
RX PubMed=15987637; DOI=10.1016/j.febslet.2005.05.080;
RA Moon B.C., Choi M.S., Kang Y.H., Kim M.C., Cheong M.S., Park C.Y.,
RA Yoo J.H., Koo S.C., Lee S.M., Lim C.O., Cho M.J., Chung W.S.;
RT "Arabidopsis ubiquitin-specific protease 6 (AtUBP6) interacts with
RT calmodulin.";
RL FEBS Lett. 579:3885-3890(2005).
CC -!- FUNCTION: Recognizes and hydrolyzes the peptide bond at the C-terminal
CC Gly of ubiquitin. Involved in the processing of poly-ubiquitin
CC precursors as well as that of ubiquitinated proteins.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide
CC and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-
CC residue protein attached to proteins as an intracellular targeting
CC signal).; EC=3.4.19.12;
CC -!- SUBUNIT: Interacts with calmodulin (CaM).
CC {ECO:0000269|PubMed:15987637}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q949Y0-1; Sequence=Displayed;
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG50872.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF302660; AAG42751.1; -; mRNA.
DR EMBL; AC025294; AAG50872.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE32705.1; -; Genomic_DNA.
DR EMBL; AY050817; AAK92752.1; -; mRNA.
DR EMBL; AY114081; AAM45129.1; -; mRNA.
DR EMBL; BT000658; AAN31805.1; -; mRNA.
DR EMBL; AY084730; AAM61304.1; -; mRNA.
DR EMBL; AK221019; BAD94710.1; -; mRNA.
DR PIR; A96556; A96556.
DR RefSeq; NP_564596.1; NM_104049.4. [Q949Y0-1]
DR AlphaFoldDB; Q949Y0; -.
DR SMR; Q949Y0; -.
DR BioGRID; 26821; 10.
DR MINT; Q949Y0; -.
DR STRING; 3702.AT1G51710.1; -.
DR MEROPS; C19.094; -.
DR iPTMnet; Q949Y0; -.
DR PaxDb; Q949Y0; -.
DR PRIDE; Q949Y0; -.
DR ProteomicsDB; 228475; -. [Q949Y0-1]
DR DNASU; 841596; -.
DR EnsemblPlants; AT1G51710.1; AT1G51710.1; AT1G51710. [Q949Y0-1]
DR GeneID; 841596; -.
DR Gramene; AT1G51710.1; AT1G51710.1; AT1G51710. [Q949Y0-1]
DR KEGG; ath:AT1G51710; -.
DR Araport; AT1G51710; -.
DR TAIR; locus:2017552; AT1G51710.
DR eggNOG; KOG1872; Eukaryota.
DR HOGENOM; CLU_017549_2_1_1; -.
DR InParanoid; Q949Y0; -.
DR OMA; MCKGGIL; -.
DR PhylomeDB; Q949Y0; -.
DR PRO; PR:Q949Y0; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q949Y0; baseline and differential.
DR Genevisible; Q949Y0; AT.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR GO; GO:0005516; F:calmodulin binding; IDA:TAIR.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IBA:GO_Central.
DR GO; GO:0070628; F:proteasome binding; IBA:GO_Central.
DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
DR GO; GO:0061136; P:regulation of proteasomal protein catabolic process; IBA:GO_Central.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR001394; Peptidase_C19_UCH.
DR InterPro; IPR000626; Ubiquitin-like_dom.
DR InterPro; IPR029071; Ubiquitin-like_domsf.
DR InterPro; IPR019954; Ubiquitin_CS.
DR InterPro; IPR044635; UBP14-like.
DR InterPro; IPR018200; USP_CS.
DR InterPro; IPR028889; USP_dom.
DR PANTHER; PTHR43982; PTHR43982; 1.
DR Pfam; PF00240; ubiquitin; 1.
DR Pfam; PF00443; UCH; 1.
DR SMART; SM00213; UBQ; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR SUPFAM; SSF54236; SSF54236; 1.
DR PROSITE; PS00299; UBIQUITIN_1; 1.
DR PROSITE; PS50053; UBIQUITIN_2; 1.
DR PROSITE; PS00972; USP_1; 1.
DR PROSITE; PS00973; USP_2; 1.
DR PROSITE; PS50235; USP_3; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Calmodulin-binding; Hydrolase; Protease;
KW Reference proteome; Thiol protease; Ubl conjugation pathway.
FT CHAIN 1..482
FT /note="Ubiquitin carboxyl-terminal hydrolase 6"
FT /id="PRO_0000313033"
FT DOMAIN 2..77
FT /note="Ubiquitin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT DOMAIN 104..478
FT /note="USP"
FT REGION 172..191
FT /note="Calmodulin-binding"
FT REGION 350..407
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 385..407
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 113
FT /note="Nucleophile"
FT ACT_SITE 430
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT MUTAGEN 113
FT /note="C->S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:15987637"
FT MUTAGEN 175
FT /note="W->R: Abolishes the calmodulin-binding."
FT /evidence="ECO:0000269|PubMed:15987637"
FT MUTAGEN 178
FT /note="L->K: Abolishes the calmodulin-binding."
FT /evidence="ECO:0000269|PubMed:15987637"
FT CONFLICT 207
FT /note="Y -> F (in Ref. 1; AAG42751)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 482 AA; 53696 MW; ECF357E9C5BEF3F7 CRC64;
MPTVSVKWQK KVLDGIEIDV SLPPYVFKAQ LYDLTGVPPE RQKIMVKGGL LKDDGDWAAI
GVKDGQKLMM MGTADEIVKA PEKAIVFAED LPEEALATNL GYSAGLVNLG NTCYMNSTVQ
CLKSVPELKS ALSNYSLAAR SNDVDQTSHM LTVATRELFG ELDRSVNAVS PSQFWMVLRK
KYPQFSQLQN GMHMQQDAEE CWTQLLYTLS QSLKAPTSSE GADAVKALFG VNLQSRLHCQ
ESGEESSETE SVYSLKCHIS HEVNHLHEGL KHGLKGELEK TSPALGRTAL YVKESLIDSL
PRYLTVQFVR FFWKRESNQK AKILRKVDYP LVLDIFDLCS EDLRKKLEAP RQKLREEEGK
KLGLQTSAKS GSKDSDVKMT DAEASANGSG ESSTVNPQEG TSSEKETHMT GIYDLVAVLT
HKGRSADSGH YVAWVKQESG KWIQYDDDNP SMQREEDITK LSGGGDWHMA YITMYKARFV
SM
