Q8LAM0 (UBP4_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ubiquitin carboxyl-terminal hydrolase 4
EC=3.4.19.12

Alternative name(s):
Deubiquitinating enzyme 4
Short name=AtUBP4
Ubiquitin thioesterase 4
Ubiquitin-specific-processing protease 4

Gene names

Name:	UBP4
Ordered Locus Names:	At2g22310
ORF Names:	T26C19.3

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	365 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
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. Required for the correct development of pollen. Ref.6 Ref.9
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).
Subcellular location	Nucleus Ref.1.
Tissue specificity	Constitutively and ubiquitously expressed. Ref.1
Sequence similarities	Belongs to the peptidase C19 family.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Molecular function	Hydrolase Protease Thiol protease
PTM	Lipoprotein Myristate
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	cysteine-type peptidase activity Inferred from electronic annotation. Source: UniProtKB-KW ubiquitin thiolesterase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select]

Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: Q8LAM0-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed Potential
	Chain	2 – 365	364	Ubiquitin carboxyl-terminal hydrolase 4		PRO_0000080695
Regions
	Motif	81 – 98	18	Bipartite nuclear localization signal Potential
Sites
	Active site	32	1	Nucleophile
	Active site	310	1	Proton acceptor By similarity
Amino acid modifications
	Lipidation	2	1	N-myristoyl glycine Ref.8
Experimental info
	Mutagenesis	32	1	C → S: Loss of activity. Ref.1
	Sequence conflict	172	1	Q → K in AAM65268. Ref.5
	Sequence conflict	334	1	E → K in AAM65268. Ref.5

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified April 26, 2005. Version 2. Checksum: 23E86CF5FDB0CE6D	FASTA	365	41,846
	10 20 30 40 50 60 MGAAGSKLEK ALGDQFPEGE RYFGFENFGN TCYCNSVLQA LYFCAPFREQ LLEHYANNKA 70 80 90 100 110 120 DAEENLLTCL ADLFSQISSQ KKKTGVIAPK RFVQRLKKQN ELFRSYMHQD AHEFLNYLLN 130 140 150 160 170 180 ELVEILEKET QATKADNETS SSPEKIANVL KAPLANGVHK EPIVTWVHKI FQGILTNETR 190 200 210 220 230 240 CLRCETVTAR DETFLDLSLD IEQNSSITSC LKNFSSTETL HAEDKFFCDK CCSLQEAQKR 250 260 270 280 290 300 MKIKKPPHIL VIHLKRFKYM EQLGRYKKLS YRVVFPLELK LSNTVDEYVD IEYSLFAVVV 310 320 330 340 350 360 HVGSGPNHGH YVSLVKSHNH WLFFDDESVE IIEESAVQTF FGSSQEYSSN TDHGYILLYE SLGTR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"AtUBP3 and AtUBP4 are two closely related Arabidopsis thaliana ubiquitin-specific proteases present in the nucleus." Chandler J.S., McArdle B., Callis J. Mol. Gen. Genet. 255:302-310(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, MUTAGENESIS OF CYS-32, TISSUE SPECIFICITY. Strain: cv. Landsberg erecta.
[2]	"Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana." Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D., Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V., Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S., Cronin L.A. , Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C. Nature 402:761-768(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]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"Full-length cDNA from Arabidopsis thaliana." Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A. Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[6]	"Ubiquitin-specific proteases from Arabidopsis thaliana: cloning of AtUBP5 and analysis of substrate specificity of AtUBP3, AtUBP4, and AtUBP5 using Escherichia coli in vivo and in vitro assays." Rao-Naik C., Chandler J.S., McArdle B., Callis J. Arch. Biochem. Biophys. 379:198-208(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"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: GENE FAMILY ORGANIZATION, NOMENCLATURE.
[8]	"Unexpected protein families including cell defense components feature in the N-myristoylome of a higher eukaryote." Boisson B., Giglione C., Meinnel T. J. Biol. Chem. 278:43418-43429(2003) [PubMed] [Europe PMC] [Abstract] Cited for: N-MYRISTOYLATION.
[9]	"The ubiquitin-specific protease subfamily UBP3/UBP4 is essential for pollen development and transmission in Arabidopsis." Doelling J.H., Phillips A.R., Soyler-Ogretim G., Wise J., Chandler J.S., Callis J., Otegui M.S., Vierstra R.D. Plant Physiol. 145:801-813(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U76846 mRNA. Translation: AAB67967.1. AC007168 Genomic DNA. Translation: AAD23612.1. CP002685 Genomic DNA. Translation: AEC07291.1. AY048261 mRNA. Translation: AAK82523.1. AY072625 mRNA. Translation: AAL62016.1. AY087731 mRNA. Translation: AAM65268.1.
IPI	IPI00539606.
PIR	B84611.
RefSeq	NP_565532.1. NM_127796.3.
UniGene	At.48505. At.71036.
3D structure databases
ProteinModelPortal	Q8LAM0.
SMR	Q8LAM0. Positions 24-339.
ModBase	Search...
Protein family/group databases
MEROPS	C19.092.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT2G22310.1; AT2G22310.1; AT2G22310.
GeneID	816763.
KEGG	ath:AT2G22310.
Organism-specific databases
GeneFarm	4912.
TAIR	At2g22310.
Phylogenomic databases
eggNOG	COG5533.
HOGENOM	HOG000231498.
InParanoid	Q8LAM0.
KO	K11842.
PhylomeDB	Q8LAM0.
ProtClustDB	CLSN2688340.
Gene expression databases
ArrayExpress	Q8LAM0.
Genevestigator	Q8LAM0.
GermOnline	AT2G22310. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR018200. Pept_C19ubi-hydrolase_C_CS. IPR001394. Peptidase_C19. [Graphical view]
Pfam	PF00443. UCH. 1 hit. [Graphical view]
PROSITE	PS00972. UCH_2_1. 1 hit. PS00973. UCH_2_2. 1 hit. PS50235. UCH_2_3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

UBP4_ARATH

Accession

Primary (citable) accession number: Q8LAM0
Secondary accession number(s): O24455

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 26, 2005
Last sequence update:	April 26, 2005
Last modified:	May 1, 2013
This is version 73 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program