UBP22_ARATH
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 03-AUG-2022, entry version 122.
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.AT5G10790.1; -.
DR MEROPS; C19.A11; -.
DR PaxDb; Q9LEW0; -.
DR PRIDE; Q9LEW0; -.
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; locus:2183760; AT5G10790.
DR eggNOG; KOG1867; Eukaryota.
DR HOGENOM; CLU_008279_11_0_1; -.
DR InParanoid; Q9LEW0; -.
DR OrthoDB; 929408at2759; -.
DR PhylomeDB; Q9LEW0; -.
DR PRO; PR:Q9LEW0; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LEW0; baseline and differential.
DR Genevisible; Q9LEW0; AT.
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:0016579; P:protein deubiquitination; IEA:InterPro.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR Gene3D; 3.30.40.10; -; 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 Pfam; PF00443; UCH; 1.
DR Pfam; PF02148; zf-UBP; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS00972; USP_1; 1.
DR PROSITE; PS50235; USP_3; 1.
DR PROSITE; PS50271; ZF_UBP; 1.
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
