ID   UBP22_ARATH             Reviewed;         557 AA.
AC   Q9LEW0; Q9FPS5;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   24-JAN-2024, entry version 128.
DE   RecName: Full=Ubiquitin C-terminal hydrolase 22 {ECO:0000305};
DE            EC=3.4.19.12 {ECO:0000305};
DE   AltName: Full=Deubiquitinating enzyme 22 {ECO:0000305};
DE            Short=AtUBP22 {ECO:0000303|PubMed:11115897};
DE   AltName: Full=Ubiquitin thioesterase 22 {ECO:0000305};
DE   AltName: Full=Ubiquitin-specific-processing protease 22 {ECO:0000305};
GN   Name=UBP22 {ECO:0000303|PubMed:11115897};
GN   OrderedLocusNames=At5g10790 {ECO:0000312|Araport:AT5G10790};
GN   ORFNames=T30N20_60 {ECO:0000312|EMBL:CAB96834.1};
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=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   IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, AND INTERACTION WITH SGF11.
RX   PubMed=29588169; DOI=10.1016/j.jmb.2018.03.018;
RA   Pfab A., Bruckmann A., Nazet J., Merkl R., Grasser K.D.;
RT   "The adaptor protein ENY2 is a component of the deubiquitination module of
RT   the Arabidopsis SAGA transcriptional co-activator complex but not of the
RT   TREX-2 complex.";
RL   J. Mol. Biol. 430:1479-1494(2018).
RN   [5]
RP   FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, INTERACTION WITH
RP   SGF11, AND SUBCELLULAR LOCATION.
RX   PubMed=30192741; DOI=10.7554/elife.37892;
RA   Nassrallah A., Rougee M., Bourbousse C., Drevensek S., Fonseca S.,
RA   Iniesto E., Ait-Mohamed O., Deton-Cabanillas A.F., Zabulon G., Ahmed I.,
RA   Stroebel D., Masson V., Lombard B., Eeckhout D., Gevaert K., Loew D.,
RA   Genovesio A., Breyton C., de Jaeger G., Bowler C., Rubio V., Barneche F.;
RT   "DET1-mediated degradation of a SAGA-like deubiquitination module controls
RT   H2Bub homeostasis.";
RL   Elife 7:0-0(2018).
CC   -!- FUNCTION: Component of a deubiquitination module (DUB module) that
CC       specifically deubiquinates monoubiquinated histone H2B (H2Bub)
CC       (PubMed:29588169, PubMed:30192741). Does not seem to be a component of
CC       the TREX-2 complex (PubMed:29588169). Seems to act independently of the
CC       SAGA multiprotein complex (PubMed:30192741). The DUB module is
CC       responsible for the major H2Bub deubiquitinase activity in Arabidopsis
CC       (PubMed:30192741). {ECO:0000269|PubMed:29588169,
CC       ECO:0000269|PubMed:30192741}.
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; Evidence={ECO:0000305};
CC   -!- SUBUNIT: Component of a deubiquitination module (DUB module) formed by
CC       ENY2, SGF11, and UBP22 in Arabidopsis (PubMed:29588169,
CC       PubMed:30192741). Interacts directly with SGF11, but not with ENY2
CC       (PubMed:29588169, PubMed:30192741). {ECO:0000269|PubMed:29588169,
CC       ECO:0000269|PubMed:30192741}.
CC   -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC       {ECO:0000269|PubMed:30192741}. Note=Displays a rather patchy
CC       distribution forming a punctuated pattern in the euchromatin
CC       (PubMed:30192741). Does not localize in the heterochromatic
CC       chromocenters or nucleolus (PubMed:30192741).
CC       {ECO:0000269|PubMed:30192741}.
CC   -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR   EMBL; AF302670; AAG42760.1; -; mRNA.
DR   EMBL; AL365234; CAB96834.1; -; Genomic_DNA.
DR   EMBL; CP002688; AED91597.1; -; Genomic_DNA.
DR   PIR; T50788; T50788.
DR   RefSeq; NP_568239.1; NM_121117.2.
DR   AlphaFoldDB; Q9LEW0; -.
DR   SMR; Q9LEW0; -.
DR   STRING; 3702.Q9LEW0; -.
DR   MEROPS; C19.A11; -.
DR   PaxDb; 3702-AT5G10790-1; -.
DR   EnsemblPlants; AT5G10790.1; AT5G10790.1; AT5G10790.
DR   GeneID; 830946; -.
DR   Gramene; AT5G10790.1; AT5G10790.1; AT5G10790.
DR   KEGG; ath:AT5G10790; -.
DR   Araport; AT5G10790; -.
DR   TAIR; AT5G10790; UBP22.
DR   eggNOG; KOG1867; Eukaryota.
DR   HOGENOM; CLU_008279_11_0_1; -.
DR   InParanoid; Q9LEW0; -.
DR   OrthoDB; 227085at2759; -.
DR   PhylomeDB; Q9LEW0; -.
DR   PRO; PR:Q9LEW0; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; Q9LEW0; baseline and differential.
DR   GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0070461; C:SAGA-type complex; IPI:TAIR.
DR   GO; GO:0004843; F:cysteine-type deubiquitinase activity; IEA:UniProtKB-EC.
DR   GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   CDD; cd02660; Peptidase_C19D; 1.
DR   Gene3D; 3.90.70.10; Cysteine proteinases; 1.
DR   Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 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   InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR   InterPro; IPR001607; Znf_UBP.
DR   PANTHER; PTHR21646:SF49; UBIQUITIN C-TERMINAL HYDROLASE 22; 1.
DR   PANTHER; PTHR21646; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE; 1.
DR   Pfam; PF00443; UCH; 1.
DR   Pfam; PF02148; zf-UBP; 1.
DR   SUPFAM; SSF54001; Cysteine proteinases; 1.
DR   SUPFAM; SSF57850; RING/U-box; 1.
DR   PROSITE; PS00972; USP_1; 1.
DR   PROSITE; PS50235; USP_3; 1.
DR   PROSITE; PS50271; ZF_UBP; 1.
DR   Genevisible; Q9LEW0; AT.
PE   1: Evidence at protein level;
KW   Hydrolase; Metal-binding; Nucleus; Protease; Reference proteome;
KW   Thiol protease; Ubl conjugation pathway; Zinc; Zinc-finger.
FT   CHAIN           1..557
FT                   /note="Ubiquitin C-terminal hydrolase 22"
FT                   /id="PRO_0000313048"
FT   DOMAIN          177..531
FT                   /note="USP"
FT   ZN_FING         36..130
FT                   /note="UBP-type; degenerate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   ACT_SITE        186
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092"
FT   ACT_SITE        491
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092"
FT   BINDING         56
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         59
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         69
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         72
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         77
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         80
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         84
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         91
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   CONFLICT        111
FT                   /note="V -> A (in Ref. 1; AAG42760)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        231
FT                   /note="V -> I (in Ref. 1; AAG42760)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        416
FT                   /note="S -> F (in Ref. 1; AAG42760)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   557 AA;  63518 MW;  3CA6C313AF0FF82C CRC64;
     MSARISFLKN PDPCNHLSDY KLRYGTDGYK SFNNLFRCFN DARIKIKLQG IDIPRCSYCS
     VYQKRLYICL ICRSISCSSH ILLHTQLNKG HDIAIDVERS ELYCCACIDQ VYDSEFDEVV
     VSKQLFGLGM SVKSGADVVA VRSNKKRRLD SQLIIGSNFL VSPRDRREKW TFPLGLRGLN
     NLGSTCFMNA VLQALVHAPP LRNFWLSGQH NRDLCPRRTM GLLCLPCDLD VIFSAMFSGD
     RTPYSPAHLL YSWWQHSTNL ATYEQQDSHE FFISLLDRIH ENEGKSKCLY QDNEECQCIT
     HKAFSGLLRS DVTCTTCGST STTYDPFIDI SLTLDSMNGF SPADCRKNRY SGGPSVNAIM
     PTLSGCLDFF TRSEKLGPDQ KLNCQSCGEK RESSKQMSIR RLPLLLCLHV KRFEHSLTRK
     TSRKIDSYLQ YPFRLNMSPY LSSSIIGKRF GNRIFAFDGE GEYDSSSSSS PSAEFEIFAV
     VTHKGMLESG HYVTYLRLKG LWYRCDDAWI NEVEEEVVRG CECYMLFYAQ ETVIQKAHKE
     LSYQVISMAD AFPFADC
//