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   24-JAN-2024, entry version 113.
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}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
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.Q67XW5; -.
DR   MEROPS; C19.A08; -.
DR   PaxDb; 3702-AT4G31670-1; -.
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; AT4G31670; UBP18.
DR   eggNOG; KOG1865; Eukaryota.
DR   HOGENOM; CLU_008279_10_3_1; -.
DR   InParanoid; Q67XW5; -.
DR   OMA; SATDHQE; -.
DR   OrthoDB; 227085at2759; -.
DR   PhylomeDB; Q67XW5; -.
DR   PRO; PR:Q67XW5; -.
DR   Proteomes; UP000006548; Chromosome 4.
DR   ExpressionAtlas; Q67XW5; baseline and differential.
DR   GO; GO:0016020; C:membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0004843; F:cysteine-type deubiquitinase activity; IEA:UniProtKB-EC.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   CDD; cd02661; Peptidase_C19E; 1.
DR   Gene3D; 6.10.140.2220; -; 1.
DR   Gene3D; 3.90.70.10; Cysteine proteinases; 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; IPR002893; Znf_MYND.
DR   PANTHER; PTHR24006; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE; 1.
DR   PANTHER; PTHR24006:SF677; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 18; 1.
DR   Pfam; PF00443; UCH; 1.
DR   Pfam; PF01753; zf-MYND; 1.
DR   SUPFAM; SSF54001; Cysteine proteinases; 1.
DR   SUPFAM; SSF144232; HIT/MYND zinc finger-like; 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.
DR   Genevisible; Q67XW5; AT.
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
//