AMSH3_ARATH
ID AMSH3_ARATH Reviewed; 507 AA.
AC Q5PNU3;
DT 10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT 10-AUG-2010, sequence version 2.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=AMSH-like ubiquitin thioesterase 3;
DE EC=3.4.19.-;
DE AltName: Full=Deubiquitinating enzyme AMSH3;
GN Name=AMSH3; OrderedLocusNames=At4g16144; ORFNames=FCAALL;
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=9461215; DOI=10.1038/35140;
RA Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
RA Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P.,
RA Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.,
RA Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R.,
RA De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M.,
RA Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M.,
RA Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A.,
RA Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D.,
RA Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A.,
RA Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S.,
RA Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G.,
RA Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.;
RT "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis
RT thaliana.";
RL Nature 391:485-488(1998).
RN [2]
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 [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;
RA Cheuk R.F., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (DEC-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, MUTAGENESIS OF
RP 411-HIS--HIS-413, INTERACTION WITH PATL1; PATL2; HSC70-1; HSC70-3; VHA-A;
RP BGLU23 AND EPSIN1, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=20543027; DOI=10.1105/tpc.110.075952;
RA Isono E., Katsiarimpa A., Mueller I.K., Anzenberger F., Stierhof Y.-D.,
RA Geldner N., Chory J., Schwechheimer C.;
RT "The deubiquitinating enzyme AMSH3 is required for intracellular
RT trafficking and vacuole biogenesis in Arabidopsis thaliana.";
RL Plant Cell 22:1826-1837(2010).
RN [6]
RP INTERACTION WITH BRO1, AND SUBCELLULAR LOCATION.
RX PubMed=26324913; DOI=10.1073/pnas.1510516112;
RA Kalinowska K., Nagel M.K., Goodman K., Cuyas L., Anzenberger F.,
RA Alkofer A., Paz-Ares J., Braun P., Rubio V., Otegui M.S., Isono E.;
RT "Arabidopsis ALIX is required for the endosomal localization of the
RT deubiquitinating enzyme AMSH3.";
RL Proc. Natl. Acad. Sci. U.S.A. 112:E5543-E5551(2015).
CC -!- FUNCTION: Zinc metalloprotease that cleaves 'Lys-48'- and 'Lys-63'-
CC linked polyubiquitin chains, but is not implicated in protein
CC degradation by the 26S proteasome, deneddylation, or desumoylation.
CC Required for intracellular trafficking (e.g. trafficking from the Golgi
CC to the vacuole and the vacuolar trafficking of endocytosed cargo),
CC endocytosis and vacuole biogenesis. {ECO:0000269|PubMed:20543027}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000250};
CC -!- SUBUNIT: Interacts with PATL1 and PATL2. May also bind to HSC70-1,
CC HSC70-3, VHA-A, BGLU23 and EPSIN1. Interacts with BRO1/ALIX
CC (PubMed:26324913). {ECO:0000269|PubMed:20543027,
CC ECO:0000269|PubMed:26324913}.
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000269|PubMed:20543027};
CC Peripheral membrane protein {ECO:0000269|PubMed:20543027}. Cytoplasm
CC {ECO:0000269|PubMed:26324913, ECO:0000305|PubMed:20543027}. Vacuole
CC membrane {ECO:0000305|PubMed:20543027}; Peripheral membrane protein
CC {ECO:0000305|PubMed:20543027}. Late endosome
CC {ECO:0000269|PubMed:26324913}. Note=Localized in late endosome when
CC associated with BRO1/ALIX. {ECO:0000269|PubMed:26324913}.
CC -!- DOMAIN: The JAMM motif is essential for the protease activity.
CC -!- DISRUPTION PHENOTYPE: Seedling growth arrest phenotype. Impaired
CC central lytic vacuole formation, autophagosomes accumulation, and mis-
CC sorting of vacuolar protein cargo to the intercellular space as well as
CC disturbed endocytosis. {ECO:0000269|PubMed:20543027}.
CC -!- SIMILARITY: Belongs to the peptidase M67C family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AL161543; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=Z97340; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; Z97340; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AL161543; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002687; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BT020354; AAV85709.1; -; mRNA.
DR AlphaFoldDB; Q5PNU3; -.
DR SMR; Q5PNU3; -.
DR BioGRID; 12597; 4.
DR STRING; 3702.AT4G16144.1; -.
DR MEROPS; M67.A06; -.
DR PaxDb; Q5PNU3; -.
DR PeptideAtlas; Q5PNU3; -.
DR PRIDE; Q5PNU3; -.
DR ProteomicsDB; 245040; -.
DR Araport; AT4G16144; -.
DR TAIR; locus:504955440; AT4G16144.
DR eggNOG; KOG2880; Eukaryota.
DR HOGENOM; CLU_023304_5_1_1; -.
DR PhylomeDB; Q5PNU3; -.
DR PRO; PR:Q5PNU3; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q5PNU3; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005768; C:endosome; IBA:GO_Central.
DR GO; GO:0016021; C:integral component of membrane; IDA:TAIR.
DR GO; GO:0005770; C:late endosome; IDA:UniProtKB.
DR GO; GO:0005774; C:vacuolar membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0070122; F:isopeptidase activity; IEA:InterPro.
DR GO; GO:0061578; F:Lys63-specific deubiquitinase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0140492; F:metal-dependent deubiquitinase activity; IEA:InterPro.
DR GO; GO:0006897; P:endocytosis; IMP:TAIR.
DR GO; GO:0046907; P:intracellular transport; IMP:TAIR.
DR GO; GO:0090316; P:positive regulation of intracellular protein transport; IMP:UniProtKB.
DR GO; GO:0044090; P:positive regulation of vacuole organization; IMP:UniProtKB.
DR GO; GO:0071108; P:protein K48-linked deubiquitination; IDA:UniProtKB.
DR GO; GO:0070536; P:protein K63-linked deubiquitination; IDA:UniProtKB.
DR GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR GO; GO:0007033; P:vacuole organization; IMP:TAIR.
DR CDD; cd08066; MPN_AMSH_like; 1.
DR InterPro; IPR000555; JAMM/MPN+_dom.
DR InterPro; IPR037518; MPN.
DR InterPro; IPR044098; STAMBP/STALP-like_MPN.
DR InterPro; IPR015063; USP8_dimer.
DR Pfam; PF01398; JAB; 1.
DR Pfam; PF08969; USP8_dimer; 1.
DR SMART; SM00232; JAB_MPN; 1.
DR PROSITE; PS50249; MPN; 1.
PE 1: Evidence at protein level;
KW Coiled coil; Cytoplasm; Endocytosis; Endosome; Hydrolase; Membrane;
KW Metal-binding; Metalloprotease; Protease; Protein transport;
KW Reference proteome; Transport; Ubl conjugation pathway; Vacuole; Zinc.
FT CHAIN 1..507
FT /note="AMSH-like ubiquitin thioesterase 3"
FT /id="PRO_0000397100"
FT DOMAIN 333..463
FT /note="MPN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT REGION 133..162
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 214..242
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 73..107
FT /evidence="ECO:0000255"
FT MOTIF 411..424
FT /note="JAMM motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT COMPBIAS 142..162
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 411
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT BINDING 413
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT BINDING 424
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT BINDING 426
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 469
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 475
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 477
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT SITE 356
FT /note="Indirect zinc-binding"
FT /evidence="ECO:0000250"
FT MUTAGEN 411..413
FT /note="HTH->ATA: In amsh3-axa; loss of ubiquitin
FT thioesterase activity and seedling growth arrest."
FT /evidence="ECO:0000269|PubMed:20543027"
FT CONFLICT 80
FT /note="K -> E (in Ref. 4; AAV85709)"
FT /evidence="ECO:0000305"
FT CONFLICT 202
FT /note="M -> W (in Ref. 4; AAV85709)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 507 AA; 57268 MW; C8E5669500FAF798 CRC64;
MKIDLNKVAR EIEVDNRIPL RNYYRIADNL LRQASIYREE KNVVDLYIML LRYSSLISET
IPFHRDYQAS LPQERLGSRK RLRAVINELE SLKPEFNQLV DKLNRVEDES RQDGSDLPVV
SYSSDAVEWP PAHKASYSRP DINKPLPTSQ PSWTYNNNLT SSSNRTQIDQ QFQKLSFDFL
PPNQATLSRH SFLGPNGLKR QMVAPKSEIK VQYPSNTDWG SADNSGLIEA GPSSSSASLN
GDSQEVSTLN SVLSLDDGRW QRHSEAVNSQ FISDATEDPF QFVGMKQPSP PPVLAQVHQE
LAQICPSKVA DPRPGPAIPS LEGKEGSNSY QHLHVPVRIM DDFLRLARSN TERNLETCGV
LAGSLKNRVF HITTLIIPKQ ESTSDSCQTL NEEEIFEVQD RLSLFPLGWI HTHPTQTCFM
SSVDLHTHYS YQIMLPEAVA IVMAPTDEST PHGIFHLSDP SGVSVIRNCQ QRGFHPHEES
EDGNPIYEHC SHVFLNAKLK YEVLDLR
