UBP2_ARATH
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 03-AUG-2022, entry version 133.
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.AT1G04860.1; -.
DR MEROPS; C19.090; -.
DR iPTMnet; Q8W4N3; -.
DR PaxDb; Q8W4N3; -.
DR PRIDE; Q8W4N3; -.
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; locus:2010622; AT1G04860.
DR eggNOG; KOG1873; Eukaryota.
DR HOGENOM; CLU_005952_1_0_1; -.
DR InParanoid; Q8W4N3; -.
DR OMA; DGMRTEE; -.
DR OrthoDB; 278083at2759; -.
DR PhylomeDB; Q8W4N3; -.
DR PRO; PR:Q8W4N3; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q8W4N3; baseline and differential.
DR Genevisible; Q8W4N3; AT.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0000502; C:proteasome complex; TAS:TAIR.
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:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; TAS:TAIR.
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 SMART; SM00290; ZnF_UBP; 1.
DR SUPFAM; SSF54001; SSF54001; 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.
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
