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Protein

Ubiquitin carboxyl-terminal hydrolase 16

Gene

UBP16

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin. Involved in the processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins. Involved in salt tolerance by modulating sodium transport activity and repressing cell death at least partially through modulating SHM1 stability and activity.1 Publication

Catalytic activityi

Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei551 – 5511NucleophilePROSITE-ProRule annotation
Active sitei807 – 8071Proton acceptorPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri74 – 11138MYND-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. cysteine-type endopeptidase activity Source: GO_Central
  2. metal ion binding Source: UniProtKB-KW
  3. ubiquitin-specific protease activity Source: GO_Central

GO - Biological processi

  1. cell proliferation Source: TAIR
  2. flower development Source: TAIR
  3. leaf development Source: TAIR
  4. proteasome-mediated ubiquitin-dependent protein catabolic process Source: GO_Central
  5. protein deubiquitination Source: UniProtKB
  6. regulation of proteasomal protein catabolic process Source: GO_Central
  7. regulation of response to salt stress Source: UniProtKB
  8. response to salt stress Source: UniProtKB
  9. root development Source: TAIR
  10. shoot system development Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciARA:AT4G24560-MONOMER.

Protein family/group databases

MEROPSiC19.A07.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase 16 (EC:3.4.19.12)
Alternative name(s):
Deubiquitinating enzyme 16
Short name:
AtUBP16
Ubiquitin thioesterase 16
Ubiquitin-specific-processing protease 16
Gene namesi
Name:UBP16
Ordered Locus Names:At4g24560
ORF Names:F22K18.240
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G24560.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei7 – 2721HelicalSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. integral component of membrane Source: UniProtKB-KW
  2. nucleus Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Disruption phenotypei

Exhibits reduced salt tolerance. Reduced shoot growth in response to salt stress.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi551 – 5511C → S: Abolishes deubiquitination activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10081008Ubiquitin carboxyl-terminal hydrolase 16PRO_0000313042Add
BLAST

Proteomic databases

PaxDbiQ9SB51.
PRIDEiQ9SB51.

Expressioni

Tissue specificityi

Expressed in flowers, siliques, rosette leaves, cauline leaves, stems and at a lower level in roots. In roots, expressed in the sieve elements.2 Publications

Inductioni

Regulated by the transcription factors NAC045 and NAC086 and up-regulated by salt stress.2 Publications

Gene expression databases

GenevestigatoriQ9SB51.

Interactioni

Subunit structurei

Interacts with SHM1 and SHM4.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
SHM1Q9SZJ53EBI-6589403,EBI-2292536
SHM4O232543EBI-6589403,EBI-6589432

Protein-protein interaction databases

BioGridi13847. 4 interactions.
IntActiQ9SB51. 2 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ9SB51.
SMRiQ9SB51. Positions 543-844.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini542 – 847306USPAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi193 – 365173Ser-richAdd
BLAST
Compositional biasi878 – 991114Ser-richAdd
BLAST

Sequence similaritiesi

Belongs to the peptidase C19 family.Curated
Contains 1 MYND-type zinc finger.PROSITE-ProRule annotation
Contains 1 USP domain.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri74 – 11138MYND-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Transmembrane, Transmembrane helix, Zinc-finger

Phylogenomic databases

eggNOGiCOG5533.
HOGENOMiHOG000242869.
InParanoidiQ9SB51.
KOiK11855.
OMAiLHSKSCL.
PhylomeDBiQ9SB51.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
IPR002893. Znf_MYND.
[Graphical view]
PfamiPF00443. UCH. 1 hit.
PF01753. zf-MYND. 1 hit.
[Graphical view]
PROSITEiPS00972. USP_1. 1 hit.
PS50235. USP_3. 1 hit.
PS01360. ZF_MYND_1. 1 hit.
PS50865. ZF_MYND_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9SB51-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLLVLDLGIS SLVLVVSLVL PLIGLFVRHK WRVAAQRREE IRRLLIHASE
60 70 80 90 100
EAARAELEAS VEFSSVAVSN VFHCPVCYCL ATTRCSRCKA VRYCSGKCQI
110 120 130 140 150
IHWRQGHKDE CHPASIVYDS EDESDSDLRL GEENGQNTPE ETLLVGPEPV
160 170 180 190 200
TIPIGESLLS NRARSPEDGN GDIADNKDDL IDKEEAVSVA ETSGSSFSGF
210 220 230 240 250
SSSPRNDSGD EISRCESFSS SESERSESLL DAHVSVEPED TCFSTIEDAP
260 270 280 290 300
SKLLSPKFVH LVESVDNLAN LPKLSVHKPE DDAGQNQSQS RSLHSLVTDR
310 320 330 340 350
HPVSADPSLK SSDFWGTALG SAERVSDSCV KSKSGRPGNS SLHFSFGSGS
360 370 380 390 400
SRDTSAAKVS EQRSSILKEA PRGTGYISDG VNLRERNAKR FDEAEIALPI
410 420 430 440 450
SSSTDALSPL DSSNLSHVTL PKSKSASSEN GSMLAPLKVG EVQLLASKAS
460 470 480 490 500
NTKKCADLMK HSPLGAKSVR VLDHQKQNGA VVQHINSLHG RSGLKASVLK
510 520 530 540 550
VVDQWTRPKS ENEMAGRHGH KGLFPYEVFA KLYTYKIEFQ PCGLINVGNS
560 570 580 590 600
CFANVVFQCL MFTPPLTTYF LQQFHSRACT KKEQCFTCGF EKLVVKAKEE
610 620 630 640 650
KSPLSPNGLL SQLQNIGIFL GNGKEEDAHE FLRFVVDTMQ SVCIKASEYD
660 670 680 690 700
MTKSSKLEDT TLIGLTFGGY LRSKIKCMKC QVKSELREKM MDLTVEIDGD
710 720 730 740 750
ISTLDDALRR FTRTEILDGE NKYRCGSCKS YERAKKKLKI TEPPNVLTIA
760 770 780 790 800
LKRFQAGKFG KLNKLIRFPE TLDLAPYVSG GSEKSHDYKL YGVIVHLDVM
810 820 830 840 850
NAAFSGHYVC YIRNQNKWYK ADDSTVVTSD VERILTKGAY MLFYARCTPT
860 870 880 890 900
PPRLAVCTKT EASNKKSRVP LPKANEKSTI SRSVSTSSPE LSSNTPGGGR
910 920 930 940 950
SGNIQSFYSS FQRLQKILEE DSASDSSSLF DSNSDECSCS TDSTSMDDFA
960 970 980 990 1000
DFIFGDHQGR AHGQSETPSP TSSSSSSSPP FTRRSPLSRS SPETYGTSRH

QLPLGGER
Length:1,008
Mass (Da):110,600
Last modified:April 30, 2000 - v1
Checksum:iF2DF3BD6E9039B9E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti183 – 1831K → N in AAG42757 (PubMed:11115897).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF302666 mRNA. Translation: AAG42757.1.
AL035356 Genomic DNA. Translation: CAA23007.1.
AL161561 Genomic DNA. Translation: CAB79366.1.
CP002687 Genomic DNA. Translation: AEE84926.1.
PIRiT05578.
RefSeqiNP_567705.1. NM_118589.2.
UniGeneiAt.2551.

Genome annotation databases

EnsemblPlantsiAT4G24560.1; AT4G24560.1; AT4G24560.
GeneIDi828558.
KEGGiath:AT4G24560.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF302666 mRNA. Translation: AAG42757.1.
AL035356 Genomic DNA. Translation: CAA23007.1.
AL161561 Genomic DNA. Translation: CAB79366.1.
CP002687 Genomic DNA. Translation: AEE84926.1.
PIRiT05578.
RefSeqiNP_567705.1. NM_118589.2.
UniGeneiAt.2551.

3D structure databases

ProteinModelPortaliQ9SB51.
SMRiQ9SB51. Positions 543-844.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi13847. 4 interactions.
IntActiQ9SB51. 2 interactions.

Protein family/group databases

MEROPSiC19.A07.

Proteomic databases

PaxDbiQ9SB51.
PRIDEiQ9SB51.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G24560.1; AT4G24560.1; AT4G24560.
GeneIDi828558.
KEGGiath:AT4G24560.

Organism-specific databases

TAIRiAT4G24560.

Phylogenomic databases

eggNOGiCOG5533.
HOGENOMiHOG000242869.
InParanoidiQ9SB51.
KOiK11855.
OMAiLHSKSCL.
PhylomeDBiQ9SB51.

Enzyme and pathway databases

BioCyciARA:AT4G24560-MONOMER.

Gene expression databases

GenevestigatoriQ9SB51.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
IPR002893. Znf_MYND.
[Graphical view]
PfamiPF00443. UCH. 1 hit.
PF01753. zf-MYND. 1 hit.
[Graphical view]
PROSITEiPS00972. USP_1. 1 hit.
PS50235. USP_3. 1 hit.
PS01360. ZF_MYND_1. 1 hit.
PS50865. ZF_MYND_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The ubiquitin-specific protease family from Arabidopsis. AtUBP1 and 2 are required for the resistance to the amino acid analog canavanine."
    Yan N., Doelling J.H., Falbel T.G., Durski A.M., Vierstra R.D.
    Plant Physiol. 124:1828-1843(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], GENE FAMILY ORGANIZATION, NOMENCLATURE.
    Strain: cv. Columbia.
  2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Ubiquitin-specific protease16 modulates salt tolerance in Arabidopsis by regulating Na(+)/H(+) antiport activity and serine hydroxymethyltransferase stability."
    Zhou H., Zhao J., Yang Y., Chen C., Liu Y., Jin X., Chen L., Li X., Deng X.W., Schumaker K.S., Guo Y.
    Plant Cell 24:5106-5122(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, INDUCTION BY SALT, TISSUE SPECIFICITY, MUTAGENESIS OF CYS-551, CATALYTIC ACTIVITY, INTERACTION WITH SHM1 AND SHM4, SUBCELLULAR LOCATION.
  5. Cited for: INDUCTION BY NAC045 AND NAC086, TISSUE SPECIFICITY.

Entry informationi

Entry nameiUBP16_ARATH
AccessioniPrimary (citable) accession number: Q9SB51
Secondary accession number(s): Q9FPS8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 14, 2008
Last sequence update: April 30, 2000
Last modified: March 3, 2015
This is version 98 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.