Q9SB51 (UBP16_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	UBP16
Ordered Locus Names:	At4g24560
ORF Names:	F22K18.240

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	1008 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.4
Catalytic activity	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). Ref.4
Subunit structure	Interacts with SHM1 and SHM4. Ref.4
Subcellular location	Membrane; Single-pass membrane protein Potential Ref.4.
Tissue specificity	Expressed in flowers, siliques, rosette leaves, cauline leaves, stems and at a lower level in roots. Ref.4
Induction	By salt stress. Ref.4
Disruption phenotype	Exhibits reduced salt tolerance. Reduced shoot growth in response to salt stress. Ref.4
Sequence similarities	Belongs to the peptidase C19 family. Contains 1 MYND-type zinc finger.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Cellular component	Membrane
Domain	Transmembrane Transmembrane helix Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Hydrolase Protease Thiol protease
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell proliferation Inferred from genetic interaction PubMed 18485060. Source: TAIR flower development Inferred from genetic interaction PubMed 18485060. Source: TAIR leaf development Inferred from genetic interaction PubMed 18485060. Source: TAIR protein deubiquitination Inferred from direct assay Ref.4. Source: UniProtKB regulation of response to salt stress Inferred from mutant phenotype Ref.4. Source: UniProtKB response to salt stress Inferred from expression pattern Ref.4. Source: UniProtKB root development Inferred from genetic interaction PubMed 18485060. Source: TAIR ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	cysteine-type peptidase activity Inferred from electronic annotation. Source: UniProtKB-KW ubiquitin thiolesterase activity Inferred from direct assay Ref.4. Source: UniProtKB zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
dl3005c	O23254	3	EBI-6589403,EBI-6589432
SHM1	Q9SZJ5	3	EBI-6589403,EBI-2292536

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1008	1008	Ubiquitin carboxyl-terminal hydrolase 16		PRO_0000313042
Regions
	Transmembrane	7 – 27	21	Helical; Potential
	Zinc finger	74 – 111	38	MYND-type
	Compositional bias	193 – 365	173	Ser-rich
	Compositional bias	878 – 991	114	Ser-rich
Sites
	Active site	551	1	Nucleophile By similarity
	Active site	807	1	Proton acceptor By similarity
Experimental info
	Mutagenesis	551	1	C → S: Abolishes deubiquitination activity. Ref.4
	Sequence conflict	183	1	K → N in AAG42757. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q9SB51 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: F2DF3BD6E9039B9E	FASTA	1,008	110,600
	10 20 30 40 50 60 MLLVLDLGIS SLVLVVSLVL PLIGLFVRHK WRVAAQRREE IRRLLIHASE EAARAELEAS 70 80 90 100 110 120 VEFSSVAVSN VFHCPVCYCL ATTRCSRCKA VRYCSGKCQI IHWRQGHKDE CHPASIVYDS 130 140 150 160 170 180 EDESDSDLRL GEENGQNTPE ETLLVGPEPV TIPIGESLLS NRARSPEDGN GDIADNKDDL 190 200 210 220 230 240 IDKEEAVSVA ETSGSSFSGF SSSPRNDSGD EISRCESFSS SESERSESLL DAHVSVEPED 250 260 270 280 290 300 TCFSTIEDAP SKLLSPKFVH LVESVDNLAN LPKLSVHKPE DDAGQNQSQS RSLHSLVTDR 310 320 330 340 350 360 HPVSADPSLK SSDFWGTALG SAERVSDSCV KSKSGRPGNS SLHFSFGSGS SRDTSAAKVS 370 380 390 400 410 420 EQRSSILKEA PRGTGYISDG VNLRERNAKR FDEAEIALPI SSSTDALSPL DSSNLSHVTL 430 440 450 460 470 480 PKSKSASSEN GSMLAPLKVG EVQLLASKAS NTKKCADLMK HSPLGAKSVR VLDHQKQNGA 490 500 510 520 530 540 VVQHINSLHG RSGLKASVLK VVDQWTRPKS ENEMAGRHGH KGLFPYEVFA KLYTYKIEFQ 550 560 570 580 590 600 PCGLINVGNS CFANVVFQCL MFTPPLTTYF LQQFHSRACT KKEQCFTCGF EKLVVKAKEE 610 620 630 640 650 660 KSPLSPNGLL SQLQNIGIFL GNGKEEDAHE FLRFVVDTMQ SVCIKASEYD MTKSSKLEDT 670 680 690 700 710 720 TLIGLTFGGY LRSKIKCMKC QVKSELREKM MDLTVEIDGD ISTLDDALRR FTRTEILDGE 730 740 750 760 770 780 NKYRCGSCKS YERAKKKLKI TEPPNVLTIA LKRFQAGKFG KLNKLIRFPE TLDLAPYVSG 790 800 810 820 830 840 GSEKSHDYKL YGVIVHLDVM NAAFSGHYVC YIRNQNKWYK ADDSTVVTSD VERILTKGAY 850 860 870 880 890 900 MLFYARCTPT PPRLAVCTKT EASNKKSRVP LPKANEKSTI SRSVSTSSPE LSSNTPGGGR 910 920 930 940 950 960 SGNIQSFYSS FQRLQKILEE DSASDSSSLF DSNSDECSCS TDSTSMDDFA DFIFGDHQGR 970 980 990 1000 AHGQSETPSP TSSSSSSSPP FTRRSPLSRS SPETYGTSRH QLPLGGER

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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(2000) [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(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-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(2012) [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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF302666 mRNA. Translation: AAG42757.1. AL035356 Genomic DNA. Translation: CAA23007.1. AL161561 Genomic DNA. Translation: CAB79366.1. CP002687 Genomic DNA. Translation: AEE84926.1.
IPI	IPI00518628.
PIR	T05578.
RefSeq	NP_567705.1. NM_118589.2.
UniGene	At.2551.
3D structure databases
ProteinModelPortal	Q9SB51.
SMR	Q9SB51. Positions 74-114, 543-844.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9SB51. 2 interactions.
Protein family/group databases
MEROPS	C19.A07.
Proteomic databases
PaxDb	Q9SB51.
PRIDE	Q9SB51.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT4G24560.1; AT4G24560.1; AT4G24560.
GeneID	828558.
KEGG	ath:AT4G24560.
Organism-specific databases
TAIR	At4g24560.
Phylogenomic databases
eggNOG	COG5533.
HOGENOM	HOG000242869.
InParanoid	Q9SB51.
KO	K11855.
OMA	RCKSYEK.
PhylomeDB	Q9SB51.
ProtClustDB	CLSN2917604.
Gene expression databases
Genevestigator	Q9SB51.
Family and domain databases
InterPro	IPR018200. Pept_C19ubi-hydrolase_C_CS. IPR001394. Peptidase_C19. IPR002893. Znf_MYND. [Graphical view]
Pfam	PF00443. UCH. 1 hit. PF01753. zf-MYND. 1 hit. [Graphical view]
PROSITE	PS00972. UCH_2_1. 1 hit. PS00973. UCH_2_2. False negative. PS50235. UCH_2_3. 1 hit. PS01360. ZF_MYND_1. 1 hit. PS50865. ZF_MYND_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

UBP16_ARATH

Accession

Primary (citable) accession number: Q9SB51
Secondary accession number(s): Q9FPS8

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	May 1, 2000
Last modified:	May 29, 2013
This is version 82 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program