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   27-MAR-2024, entry version 130.
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.Q8LAM0; -.
DR   MEROPS; C19.092; -.
DR   iPTMnet; Q8LAM0; -.
DR   PaxDb; 3702-AT2G22310-2; -.
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   TAIR; AT2G22310; UBP4.
DR   eggNOG; KOG1864; Eukaryota.
DR   HOGENOM; CLU_008279_2_0_1; -.
DR   InParanoid; Q8LAM0; -.
DR   OMA; KYWVKYL; -.
DR   OrthoDB; 227085at2759; -.
DR   PhylomeDB; Q8LAM0; -.
DR   PRO; PR:Q8LAM0; -.
DR   Proteomes; UP000006548; Chromosome 2.
DR   ExpressionAtlas; Q8LAM0; baseline and differential.
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:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   CDD; cd02663; Peptidase_C19G; 1.
DR   Gene3D; 3.90.70.10; Cysteine proteinases; 1.
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   PANTHER; PTHR24006; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE; 1.
DR   PANTHER; PTHR24006:SF733; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE-RELATED; 1.
DR   Pfam; PF00443; UCH; 1.
DR   SUPFAM; SSF54001; Cysteine proteinases; 1.
DR   PROSITE; PS00972; USP_1; 1.
DR   PROSITE; PS00973; USP_2; 1.
DR   PROSITE; PS50235; USP_3; 1.
DR   Genevisible; Q8LAM0; AT.
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
//