UBP18_ARATH
ID UBP18_ARATH Reviewed; 631 AA.
AC Q67XW5; O81780; Q682A0;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 2.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 18;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 18;
DE Short=AtUBP18;
DE AltName: Full=Ubiquitin thioesterase 18;
DE AltName: Full=Ubiquitin-specific-processing protease 18;
GN Name=UBP18; OrderedLocusNames=At4g31670; ORFNames=F28M20.140;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [2]
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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
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).
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 (By similarity).
CC {ECO:0000250}.
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: Membrane {ECO:0000305}; Single-pass membrane
CC protein {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR EMBL; AL031004; CAA19756.1; -; Genomic_DNA.
DR EMBL; AL161579; CAB79885.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85943.1; -; Genomic_DNA.
DR EMBL; AY142532; AAN13075.1; -; mRNA.
DR EMBL; AK175467; BAD43230.1; -; mRNA.
DR EMBL; AK176703; BAD44466.1; -; mRNA.
DR PIR; T05103; T05103.
DR RefSeq; NP_194895.1; NM_119316.5.
DR AlphaFoldDB; Q67XW5; -.
DR SMR; Q67XW5; -.
DR BioGRID; 14581; 1.
DR STRING; 3702.AT4G31670.1; -.
DR MEROPS; C19.A08; -.
DR PaxDb; Q67XW5; -.
DR PRIDE; Q67XW5; -.
DR ProteomicsDB; 233049; -.
DR EnsemblPlants; AT4G31670.1; AT4G31670.1; AT4G31670.
DR GeneID; 829295; -.
DR Gramene; AT4G31670.1; AT4G31670.1; AT4G31670.
DR KEGG; ath:AT4G31670; -.
DR Araport; AT4G31670; -.
DR TAIR; locus:2124809; AT4G31670.
DR eggNOG; KOG1865; Eukaryota.
DR HOGENOM; CLU_008279_10_3_1; -.
DR InParanoid; Q67XW5; -.
DR OMA; SATDHQE; -.
DR OrthoDB; 561804at2759; -.
DR PhylomeDB; Q67XW5; -.
DR PRO; PR:Q67XW5; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q67XW5; baseline and differential.
DR Genevisible; Q67XW5; AT.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
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:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
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; IPR002893; Znf_MYND.
DR Pfam; PF00443; UCH; 1.
DR Pfam; PF01753; zf-MYND; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS00972; USP_1; 1.
DR PROSITE; PS50235; USP_3; 1.
DR PROSITE; PS01360; ZF_MYND_1; 1.
DR PROSITE; PS50865; ZF_MYND_2; 1.
PE 2: Evidence at transcript level;
KW Hydrolase; Membrane; Metal-binding; Protease; Reference proteome;
KW Thiol protease; Transmembrane; Transmembrane helix;
KW Ubl conjugation pathway; Zinc; Zinc-finger.
FT CHAIN 1..631
FT /note="Ubiquitin carboxyl-terminal hydrolase 18"
FT /id="PRO_0000313044"
FT TRANSMEM 10..30
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 168..474
FT /note="USP"
FT ZN_FING 61..98
FT /note="MYND-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT REGION 518..631
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 532..548
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 560..590
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 600..614
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 177
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092"
FT ACT_SITE 433
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092"
FT BINDING 61
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 64
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 72
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 75
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 81
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 85
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 94
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 98
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT CONFLICT 432
FT /note="G -> S (in Ref. 4; BAD43230)"
FT /evidence="ECO:0000305"
FT CONFLICT 550
FT /note="S -> P (in Ref. 4; BAD44466)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 631 AA; 70753 MW; 4C875C228588A0BE CRC64;
MHEVGFPLDL SVFTRLIATL FFLAVGVFYF LKNTAAKYFD IGAAAAGGFD RDFMAVDAED
CSVCGNFSTK KCSRCKSVRY CSAECQRSDW SSGHQRNCRD YGITTLTPSA KNGLRFRASP
FGDSSASSIA LISERGQNKS SLKPREVLFP YEEFVEYFNW DNPELAPCGL MNCGNSCFAN
VILQCLSWTR PLVAYLLEKG HKRECMRNDW CFLCEFQTHV ERASQSRFPF SPMNIISRLT
NIGGTLGYGR QEDAHEFMRY AIDMMQSVCL DEFGGEKIVP PRSQETTLIQ YIFGGLLQSQ
VQCTVCNHVS DQYENMMDLI VEMHGDAGSL EECLDQFTAE EWLHGDNMYK CDRCSDYVKA
CKRLTIRRAP NILTIALKRY QGGRYGKLNK RISFPETLDL NPYMSEGGDG SDVYKLYAVI
VHLDMLNASF FGHYICYIKD FCGNWYRIDD SEIESVELED VLSQRAYMLL YSRIQARSSS
SCLRSEVKDE KKTDTLDTES CVKELVESSM VGAIESRSST HATIEDPVCE QSPSPSPSPS
PSPSPSPSPS VLASECCSEV ERIDTLDSES NSSIDDSATD HQEDVANGNK DPEVKYQAAD
SWSDPTTSTP LVCTKSKPPV RDMDTKMIDA Q
