UBP4_ARATH
ID UBP4_ARATH Reviewed; 365 AA.
AC Q8LAM0; O24455;
DT 26-APR-2005, integrated into UniProtKB/Swiss-Prot.
DT 26-APR-2005, sequence version 2.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 4;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 4;
DE Short=AtUBP4;
DE AltName: Full=Ubiquitin thioesterase 4;
DE AltName: Full=Ubiquitin-specific-processing protease 4;
GN Name=UBP4; OrderedLocusNames=At2g22310; ORFNames=T26C19.3;
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], SUBCELLULAR LOCATION, MUTAGENESIS OF CYS-32,
RP AND TISSUE SPECIFICITY.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=9268021; DOI=10.1007/s004380050501;
RA Chandler J.S., McArdle B., Callis J.;
RT "AtUBP3 and AtUBP4 are two closely related Arabidopsis thaliana ubiquitin-
RT specific proteases present in the nucleus.";
RL Mol. Gen. Genet. 255:302-310(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
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 FUNCTION.
RX PubMed=10898935; DOI=10.1006/abbi.2000.1874;
RA Rao-Naik C., Chandler J.S., McArdle B., Callis J.;
RT "Ubiquitin-specific proteases from Arabidopsis thaliana: cloning of AtUBP5
RT and analysis of substrate specificity of AtUBP3, AtUBP4, and AtUBP5 using
RT Escherichia coli in vivo and in vitro assays.";
RL Arch. Biochem. Biophys. 379:198-208(2000).
RN [7]
RP GENE FAMILY ORGANIZATION, AND NOMENCLATURE.
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 [8]
RP MYRISTOYLATION AT GLY-2.
RX PubMed=12912986; DOI=10.1074/jbc.m307321200;
RA Boisson B., Giglione C., Meinnel T.;
RT "Unexpected protein families including cell defense components feature in
RT the N-myristoylome of a higher eukaryote.";
RL J. Biol. Chem. 278:43418-43429(2003).
RN [9]
RP FUNCTION.
RX PubMed=17905865; DOI=10.1104/pp.106.095323;
RA Doelling J.H., Phillips A.R., Soyler-Ogretim G., Wise J., Chandler J.S.,
RA Callis J., Otegui M.S., Vierstra R.D.;
RT "The ubiquitin-specific protease subfamily UBP3/UBP4 is essential for
RT pollen development and transmission in Arabidopsis.";
RL Plant Physiol. 145:801-813(2007).
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. Required for the
CC correct development of pollen. {ECO:0000269|PubMed:10898935,
CC ECO:0000269|PubMed:17905865}.
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 -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:9268021}.
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=Q8LAM0-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Constitutively and ubiquitously expressed.
CC {ECO:0000269|PubMed:9268021}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR EMBL; U76846; AAB67967.1; -; mRNA.
DR EMBL; AC007168; AAD23612.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC07291.1; -; Genomic_DNA.
DR EMBL; AY048261; AAK82523.1; -; mRNA.
DR EMBL; AY072625; AAL62016.1; -; mRNA.
DR EMBL; AY087731; AAM65268.1; -; mRNA.
DR PIR; B84611; B84611.
DR RefSeq; NP_565532.1; NM_127796.3. [Q8LAM0-1]
DR AlphaFoldDB; Q8LAM0; -.
DR SMR; Q8LAM0; -.
DR STRING; 3702.AT2G22310.2; -.
DR MEROPS; C19.092; -.
DR iPTMnet; Q8LAM0; -.
DR PaxDb; Q8LAM0; -.
DR PRIDE; Q8LAM0; -.
DR ProteomicsDB; 245256; -. [Q8LAM0-1]
DR EnsemblPlants; AT2G22310.1; AT2G22310.1; AT2G22310. [Q8LAM0-1]
DR GeneID; 816763; -.
DR Gramene; AT2G22310.1; AT2G22310.1; AT2G22310. [Q8LAM0-1]
DR KEGG; ath:AT2G22310; -.
DR Araport; AT2G22310; -.
DR eggNOG; KOG1864; Eukaryota.
DR HOGENOM; CLU_008279_2_0_1; -.
DR InParanoid; Q8LAM0; -.
DR OMA; ATVVHCG; -.
DR PhylomeDB; Q8LAM0; -.
DR PRO; PR:Q8LAM0; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q8LAM0; baseline and differential.
DR Genevisible; Q8LAM0; AT.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IBA:GO_Central.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; IBA:GO_Central.
DR GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR001394; Peptidase_C19_UCH.
DR InterPro; IPR018200; USP_CS.
DR InterPro; IPR028889; USP_dom.
DR Pfam; PF00443; UCH; 1.
DR SUPFAM; SSF54001; SSF54001; 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; Hydrolase; Lipoprotein; Myristate; Nucleus; Protease;
KW Reference proteome; Thiol protease; Ubl conjugation pathway.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000255"
FT CHAIN 2..365
FT /note="Ubiquitin carboxyl-terminal hydrolase 4"
FT /id="PRO_0000080695"
FT DOMAIN 23..362
FT /note="USP"
FT MOTIF 81..98
FT /note="Bipartite nuclear localization signal"
FT /evidence="ECO:0000255"
FT ACT_SITE 32
FT /note="Nucleophile"
FT ACT_SITE 310
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT LIPID 2
FT /note="N-myristoyl glycine"
FT /evidence="ECO:0000269|PubMed:12912986"
FT MUTAGEN 32
FT /note="C->S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:9268021"
FT CONFLICT 172
FT /note="Q -> K (in Ref. 5; AAM65268)"
FT /evidence="ECO:0000305"
FT CONFLICT 334
FT /note="E -> K (in Ref. 5; AAM65268)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 365 AA; 41846 MW; 23E86CF5FDB0CE6D CRC64;
MGAAGSKLEK ALGDQFPEGE RYFGFENFGN TCYCNSVLQA LYFCAPFREQ LLEHYANNKA
DAEENLLTCL ADLFSQISSQ KKKTGVIAPK RFVQRLKKQN ELFRSYMHQD AHEFLNYLLN
ELVEILEKET QATKADNETS SSPEKIANVL KAPLANGVHK EPIVTWVHKI FQGILTNETR
CLRCETVTAR DETFLDLSLD IEQNSSITSC LKNFSSTETL HAEDKFFCDK CCSLQEAQKR
MKIKKPPHIL VIHLKRFKYM EQLGRYKKLS YRVVFPLELK LSNTVDEYVD IEYSLFAVVV
HVGSGPNHGH YVSLVKSHNH WLFFDDESVE IIEESAVQTF FGSSQEYSSN TDHGYILLYE
SLGTR
