ID   UBP2_ARATH              Reviewed;         961 AA.
AC   Q8W4N3; Q9MAT4;
DT   26-APR-2005, integrated into UniProtKB/Swiss-Prot.
DT   26-APR-2005, sequence version 2.
DT   27-MAR-2024, entry version 141.
DE   RecName: Full=Ubiquitin carboxyl-terminal hydrolase 2;
DE            EC=3.4.19.12;
DE   AltName: Full=Deubiquitinating enzyme 2;
DE            Short=AtUBP2;
DE   AltName: Full=Ubiquitin thioesterase 2;
DE   AltName: Full=Ubiquitin-specific-processing protease 2;
GN   Name=UBP2; OrderedLocusNames=At1g04860; ORFNames=F13M7.15;
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, NOMENCLATURE,
RP   FUNCTION, AND MUTAGENESIS OF CYS-240.
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   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   STRAIN=cv. Landsberg erecta;
RX   PubMed=17272265; DOI=10.1074/mcp.m600408-mcp200;
RA   Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
RT   "Multidimensional protein identification technology (MudPIT) analysis of
RT   ubiquitinated proteins in plants.";
RL   Mol. Cell. Proteomics 6:601-610(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. Is involved in
CC       resistance to the arginine analog canavanine (CAN).
CC       {ECO:0000269|PubMed:11115897}.
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   -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR   EMBL; AF302659; AAG42750.1; -; mRNA.
DR   EMBL; AC004809; AAF40451.1; -; Genomic_DNA.
DR   EMBL; CP002684; AEE27752.1; -; Genomic_DNA.
DR   EMBL; AY062463; AAL32541.1; -; mRNA.
DR   PIR; H86181; H86181.
DR   RefSeq; NP_563719.1; NM_100364.4.
DR   AlphaFoldDB; Q8W4N3; -.
DR   STRING; 3702.Q8W4N3; -.
DR   MEROPS; C19.090; -.
DR   iPTMnet; Q8W4N3; -.
DR   PaxDb; 3702-AT1G04860-1; -.
DR   ProteomicsDB; 233057; -.
DR   EnsemblPlants; AT1G04860.1; AT1G04860.1; AT1G04860.
DR   GeneID; 839397; -.
DR   Gramene; AT1G04860.1; AT1G04860.1; AT1G04860.
DR   KEGG; ath:AT1G04860; -.
DR   Araport; AT1G04860; -.
DR   TAIR; AT1G04860; UBP2.
DR   eggNOG; KOG1873; Eukaryota.
DR   HOGENOM; CLU_005952_1_0_1; -.
DR   InParanoid; Q8W4N3; -.
DR   OMA; MAAGHYV; -.
DR   OrthoDB; 227085at2759; -.
DR   PhylomeDB; Q8W4N3; -.
DR   PRO; PR:Q8W4N3; -.
DR   Proteomes; UP000006548; Chromosome 1.
DR   ExpressionAtlas; Q8W4N3; baseline and differential.
DR   GO; GO:0000502; C:proteasome complex; TAS: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:0006511; P:ubiquitin-dependent protein catabolic process; TAS:TAIR.
DR   Gene3D; 3.90.70.10; Cysteine proteinases; 2.
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; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE; 1.
DR   PANTHER; PTHR21646:SF39; UBIQUITINYL HYDROLASE 1; 1.
DR   Pfam; PF00443; UCH; 1.
DR   Pfam; PF02148; zf-UBP; 1.
DR   SMART; SM00290; ZnF_UBP; 1.
DR   SUPFAM; SSF54001; Cysteine proteinases; 1.
DR   SUPFAM; SSF57850; RING/U-box; 1.
DR   PROSITE; PS00972; USP_1; 1.
DR   PROSITE; PS00973; USP_2; 1.
DR   PROSITE; PS50235; USP_3; 1.
DR   PROSITE; PS50271; ZF_UBP; 1.
DR   Genevisible; Q8W4N3; AT.
PE   1: Evidence at protein level;
KW   Hydrolase; Metal-binding; Protease; Reference proteome; Thiol protease;
KW   Ubl conjugation pathway; Zinc; Zinc-finger.
FT   CHAIN           1..961
FT                   /note="Ubiquitin carboxyl-terminal hydrolase 2"
FT                   /id="PRO_0000080693"
FT   DOMAIN          231..957
FT                   /note="USP"
FT   ZN_FING         48..183
FT                   /note="UBP-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   REGION          1..36
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          85..105
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          387..418
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          744..770
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          784..826
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        395..410
FT                   /note="Basic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        787..826
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        240
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   ACT_SITE        907
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   BINDING         50
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         52
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         74
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="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         113
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         116
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         121
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         133
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         137
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         143
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         157
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         160
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   MUTAGEN         240
FT                   /note="C->A,S: Confers CAN sensitivity."
FT                   /evidence="ECO:0000269|PubMed:11115897"
FT   CONFLICT        261
FT                   /note="K -> E (in Ref. 4; AAL32541)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        653
FT                   /note="E -> K (in Ref. 4; AAL32541)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   961 AA;  105152 MW;  E4881E31F1ADE2C7 CRC64;
     MGKKAKKKAR APTKEIQTME ISKKVSEEPP SQAGEIAEGD VKAVKETQAC VHFDKALNLE
     KVLDKIKSSR QIKCAECNEG VYGKRGTKAK GSKGKKDFSS SDPKSNNKAI WLCLECGCYV
     CGGVGLPNGP QSHVLRHSRV TRHRLVIQWE NPQLRWCFPC QLLLPVEKED NGEKKDVLSE
     VVKLIKGRSL NNLASSDIED QCSGSGSITS DIKLEGAVTS DIEARDGYVV RGLVNLGNTC
     FFNSIMQNLL SLDRLRDHFL KENGSGVGGP LASSLRKLFT ETKPEAGLKS VINPRAFFGS
     FCSKAPQFRG YDQHDSHELL RCLLDSLSTE ESALRKKRGV SDNDEKSTTL IESVFGGETS
     SIVSCMECGH SSKVYEPFLD LSLPVPFKKS PPKKPQPVSR AKKAKLPPKR VPKNVSKVSK
     VSKVLPGMVL SELNSSGKSM AVTADSDTSC SSLAPLDNGP VLETPSVLTL DNNQASESAS
     QSDTGFDGSW LDFIGPETSG DETNLDMQED GIDNVITAEV NQIVPSPNIV ANSSVSSGDQ
     TLEGNTERLM QDYEEIAKAE ANLDEKDVQA MQSDECPATS GISAEFSQAS CIGCDPGIGE
     SSSSVNPWDE EELPLVVADS QILYMPYKEI SCNDKSVEGE CEASSSFVTG DHEPQNSDFV
     DFGGLFDEPE TTEGPVFGPP SKAEASGVGF MAFSSESDPE EIDDSDLPVS VERCLGHFTK
     HEILSDDNAW NCENCSKNLK LQRLREKRKS NEDESRSSNT SNGWVKENED EGFGETEILA
     VKQDPNDTSC VKDHSSDGRK AARIHSADES ESKGTQDEDE DSEKVITVKR DATKKVLINK
     APPVLTIHLK RFSQDLRGRL SKLNGHVAFK EVIDLRQYMD SRCSGEDPPV YRLAGLVEHS
     GTMRGGHYVA YVRGGQRVKE TDSSSTAWYN VSDAYVRQVS LEKVLHSEAY ILFYERIFSQ
     E
//