ID UBP16_ARATH Reviewed; 1008 AA.
AC Q9SB51; Q9FPS8;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 27-MAR-2024, entry version 142.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 16;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 16;
DE Short=AtUBP16;
DE AltName: Full=Ubiquitin thioesterase 16;
DE AltName: Full=Ubiquitin-specific-processing protease 16;
GN Name=UBP16; OrderedLocusNames=At4g24560; ORFNames=F22K18.240;
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, AND NOMENCLATURE.
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=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 FUNCTION, DISRUPTION PHENOTYPE, INDUCTION BY SALT, TISSUE SPECIFICITY,
RP MUTAGENESIS OF CYS-551, CATALYTIC ACTIVITY, INTERACTION WITH SHM1 AND SHM4,
RP AND SUBCELLULAR LOCATION.
RX PubMed=23232097; DOI=10.1105/tpc.112.106393;
RA Zhou H., Zhao J., Yang Y., Chen C., Liu Y., Jin X., Chen L., Li X.,
RA Deng X.W., Schumaker K.S., Guo Y.;
RT "Ubiquitin-specific protease16 modulates salt tolerance in Arabidopsis by
RT regulating Na(+)/H(+) antiport activity and serine hydroxymethyltransferase
RT stability.";
RL Plant Cell 24:5106-5122(2012).
RN [5]
RP FUNCTION, AND INTERACTION WITH HIPP27.
RX PubMed=23857362; DOI=10.4161/psb.25680;
RA Zhao J., Zhou H., Li Y.;
RT "UBIQUITIN-SPECIFIC PROTEASE16 interacts with a HEAVY METAL ASSOCIATED
RT ISOPRENYLATED PLANT PROTEIN27 and modulates cadmium tolerance.";
RL Plant Signal. Behav. 8:E25680-E25680(2013).
RN [6]
RP INDUCTION BY NAC045 AND NAC086, AND TISSUE SPECIFICITY.
RX PubMed=25081480; DOI=10.1126/science.1253736;
RA Furuta K.M., Yadav S.R., Lehesranta S., Belevich I., Miyashima S.,
RA Heo J.O., Vaten A., Lindgren O., De Rybel B., Van Isterdael G.,
RA Somervuo P., Lichtenberger R., Rocha R., Thitamadee S., Taehtiharju S.,
RA Auvinen P., Beeckman T., Jokitalo E., Helariutta Y.;
RT "Plant development. Arabidopsis NAC45/86 direct sieve element morphogenesis
RT culminating in enucleation.";
RL Science 345:933-937(2014).
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. Involved in salt
CC tolerance by modulating sodium transport activity and repressing cell
CC death at least partially through modulating SHM1 stability and activity
CC (PubMed:23232097). Involved in cadmium tolerance by interacting with
CC HIPP27 and probably modulating its stability (PubMed:23857362).
CC {ECO:0000269|PubMed:23232097, ECO:0000269|PubMed:23857362}.
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; Evidence={ECO:0000269|PubMed:23232097};
CC -!- SUBUNIT: Interacts with SHM1 and SHM4 (PubMed:23232097). Interacts with
CC HIPP27 (PubMed:23857362). {ECO:0000269|PubMed:23232097,
CC ECO:0000269|PubMed:23857362}.
CC -!- INTERACTION:
CC Q9SB51; Q9SZJ5: SHM1; NbExp=3; IntAct=EBI-6589403, EBI-2292536;
CC Q9SB51; O23254: SHM4; NbExp=3; IntAct=EBI-6589403, EBI-6589432;
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000305}; Single-pass membrane
CC protein {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Expressed in flowers, siliques, rosette leaves,
CC cauline leaves, stems and at a lower level in roots. In roots,
CC expressed in the sieve elements. {ECO:0000269|PubMed:23232097,
CC ECO:0000269|PubMed:25081480}.
CC -!- INDUCTION: Regulated by the transcription factors NAC045 and NAC086 and
CC up-regulated by salt stress. {ECO:0000269|PubMed:23232097,
CC ECO:0000269|PubMed:25081480}.
CC -!- DISRUPTION PHENOTYPE: Exhibits reduced salt tolerance. Reduced shoot
CC growth in response to salt stress. {ECO:0000269|PubMed:23232097}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR EMBL; AF302666; AAG42757.1; -; mRNA.
DR EMBL; AL035356; CAA23007.1; -; Genomic_DNA.
DR EMBL; AL161561; CAB79366.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE84926.1; -; Genomic_DNA.
DR PIR; T05578; T05578.
DR RefSeq; NP_567705.1; NM_118589.3.
DR AlphaFoldDB; Q9SB51; -.
DR SMR; Q9SB51; -.
DR BioGRID; 13847; 4.
DR IntAct; Q9SB51; 2.
DR STRING; 3702.Q9SB51; -.
DR MEROPS; C19.A07; -.
DR PaxDb; 3702-AT4G24560-1; -.
DR ProteomicsDB; 228481; -.
DR EnsemblPlants; AT4G24560.1; AT4G24560.1; AT4G24560.
DR GeneID; 828558; -.
DR Gramene; AT4G24560.1; AT4G24560.1; AT4G24560.
DR KEGG; ath:AT4G24560; -.
DR Araport; AT4G24560; -.
DR TAIR; AT4G24560; UBP16.
DR eggNOG; KOG1865; Eukaryota.
DR HOGENOM; CLU_007397_1_1_1; -.
DR InParanoid; Q9SB51; -.
DR OMA; LFYARCT; -.
DR OrthoDB; 227085at2759; -.
DR PhylomeDB; Q9SB51; -.
DR PRO; PR:Q9SB51; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9SB51; baseline and differential.
DR Genevisible; Q9SB51; AT.
DR GO; GO:0016020; C:membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0051301; P:cell division; IGI:TAIR.
DR GO; GO:0009908; P:flower development; IGI:TAIR.
DR GO; GO:0048366; P:leaf development; IGI:TAIR.
DR GO; GO:0016579; P:protein deubiquitination; IDA:UniProtKB.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:1901000; P:regulation of response to salt stress; IMP:UniProtKB.
DR GO; GO:0009651; P:response to salt stress; IEP:UniProtKB.
DR GO; GO:0048364; P:root development; IGI:TAIR.
DR GO; GO:0048367; P:shoot system development; IGI:TAIR.
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:SF874; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 16; 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.
PE 1: Evidence at protein 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..1008
FT /note="Ubiquitin carboxyl-terminal hydrolase 16"
FT /id="PRO_0000313042"
FT TRANSMEM 7..27
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 542..847
FT /note="USP"
FT ZN_FING 74..111
FT /note="MYND-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT REGION 122..149
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 159..178
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 187..233
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 275..309
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 326..379
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 859..905
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 952..1008
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 189..208
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 209..233
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 281..297
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 332..362
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 874..905
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 962..998
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 551
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092"
FT ACT_SITE 807
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092"
FT BINDING 74
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 77
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="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 88
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 94
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 98
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 107
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 111
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT MUTAGEN 551
FT /note="C->S: Abolishes deubiquitination activity."
FT /evidence="ECO:0000269|PubMed:23232097"
FT CONFLICT 183
FT /note="K -> N (in Ref. 1; AAG42757)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1008 AA; 110600 MW; F2DF3BD6E9039B9E CRC64;
MLLVLDLGIS SLVLVVSLVL PLIGLFVRHK WRVAAQRREE IRRLLIHASE EAARAELEAS
VEFSSVAVSN VFHCPVCYCL ATTRCSRCKA VRYCSGKCQI IHWRQGHKDE CHPASIVYDS
EDESDSDLRL GEENGQNTPE ETLLVGPEPV TIPIGESLLS NRARSPEDGN GDIADNKDDL
IDKEEAVSVA ETSGSSFSGF SSSPRNDSGD EISRCESFSS SESERSESLL DAHVSVEPED
TCFSTIEDAP SKLLSPKFVH LVESVDNLAN LPKLSVHKPE DDAGQNQSQS RSLHSLVTDR
HPVSADPSLK SSDFWGTALG SAERVSDSCV KSKSGRPGNS SLHFSFGSGS SRDTSAAKVS
EQRSSILKEA PRGTGYISDG VNLRERNAKR FDEAEIALPI SSSTDALSPL DSSNLSHVTL
PKSKSASSEN GSMLAPLKVG EVQLLASKAS NTKKCADLMK HSPLGAKSVR VLDHQKQNGA
VVQHINSLHG RSGLKASVLK VVDQWTRPKS ENEMAGRHGH KGLFPYEVFA KLYTYKIEFQ
PCGLINVGNS CFANVVFQCL MFTPPLTTYF LQQFHSRACT KKEQCFTCGF EKLVVKAKEE
KSPLSPNGLL SQLQNIGIFL GNGKEEDAHE FLRFVVDTMQ SVCIKASEYD MTKSSKLEDT
TLIGLTFGGY LRSKIKCMKC QVKSELREKM MDLTVEIDGD ISTLDDALRR FTRTEILDGE
NKYRCGSCKS YERAKKKLKI TEPPNVLTIA LKRFQAGKFG KLNKLIRFPE TLDLAPYVSG
GSEKSHDYKL YGVIVHLDVM NAAFSGHYVC YIRNQNKWYK ADDSTVVTSD VERILTKGAY
MLFYARCTPT PPRLAVCTKT EASNKKSRVP LPKANEKSTI SRSVSTSSPE LSSNTPGGGR
SGNIQSFYSS FQRLQKILEE DSASDSSSLF DSNSDECSCS TDSTSMDDFA DFIFGDHQGR
AHGQSETPSP TSSSSSSSPP FTRRSPLSRS SPETYGTSRH QLPLGGER
//
