O96612 (UBPB_DICDI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ubiquitin hydrolase B
EC=3.4.19.12

Gene names

Name:	ubpB
ORF Names:	DDB_G0275021

Organism

Dictyostelium discoideum (Slime mold) [Reference proteome]

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	451 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Required for proper prespore cell patterning. Plays a role in stabilizing mkkA by preventing it from being targeted for degradation. ubcB and ubpB differentially control ubiquitination/deubiquitination and degradation of mkkA in a cell-type-specific and temporally regulated manner. Ref.1
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).
Subunit structure	Interacts with mkkA (via F-box/WD40 domains). Ref.1
Developmental stage	Found at low levels in vegetative cells and at higher levels during aggregation and mound formation (4 and 8 hours of development). Ref.1
Disruption phenotype	Null cells differentiate into prestalk cells preferentially. They develop precociously and exhibit abnormal cell-type patterning with an increase in the prestalk domain and reduction in the prespore domain in the slug, and spore domain in a fruiting body. Null cells do not form the normal spherical sori seen in mature wild-type fruiting bodies. Instead, the sori remain elongated, similar to those seen in wild-type fruiting bodies that are not fully mature. The upper and lower cups of the fruiting body, which are derived from prestalk cells and anterior-like cells, are enlarged. The spore-containing region is reduced. Null cells form fruiting bodies at approximately 17 hours and exhibit precocious expression of the spore marker. The expression levels of the prespore/spore markers are lower in null cells compared to wild-type cells, whereas expression of the prestalk/stalk marker is elevated slightly. The loss of gene function, might lead to increased mkkA ubiquitination and a more rapid turnover of mkkA. This should result in a reduced level of mkkA activity, producing the above mentioned mkkA null cell type phenotype. Ref.1
Sequence similarities	Belongs to the peptidase C19 family.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Molecular function	Hydrolase Protease Thiol protease
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	protein deubiquitination Inferred from direct assay Ref.1. Source: dictyBase ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro
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...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 451	451	Ubiquitin hydrolase B		PRO_0000389021
Regions
	Compositional bias	88 – 91	4	Poly-Thr
	Compositional bias	92 – 95	4	Poly-Ser
	Compositional bias	136 – 144	9	Poly-Gln
Sites
	Active site	399	1	Nucleophile By similarity
	Active site	408	1	Proton acceptor By similarity

Sequences

	Sequence		Length	Mass (Da)
	O96612 [UniParc]. Last modified May 1, 1999. Version 1. Checksum: DADCD2CD07AFBFD7	FASTA	451	51,134
	10 20 30 40 50 60 MKNIEEMPSK SQLVAHRSRG LINTSNTCFM NVILQSLTGC QLFLRVIKNL SDLEDLGKYP 70 80 90 100 110 120 TLHSFNQFYT EYFSNPTSNI LNNNSNSTTT TSSSSTTATT TSTSNNNKSQ TPTSPIQQHH 130 140 150 160 170 180 QSQTNGLSNQ PSVATQSQQQ QQPQPPINPK HFNDLVKSFN SKVSPVPQTT VSPHSMVQVS 190 200 210 220 230 240 KKKLKLQLYN NSLPQTICQQ DAQEFLVFLL DLIHEEFLTL IKDIDIPKED DKSTPTSTSI 250 260 270 280 290 300 VDDNWEVVGK KGKTAIITNS QQELPKTPIS QIFSGVLRSS FNRTGSKESI TVEPFYCLHL 310 320 330 340 350 360 DIRPEEINSL EDALKFFMKP EIIEGYTCST KKIEISASKS WSFESLPRIL IVHFKRFAFE 370 380 390 400 410 420 SDTSKKLDKL IRFPTQLSLS TASNHQTQKK YSLFSVVSHH GRGLSQGHYT CDIYQPQQAQ 430 440 450 WIRYDDSTFT EVKEQDVLNR EAYLLLYQLV N

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A novel, putative MEK kinase controls developmental timing and spatial patterning in Dictyostelium and is regulated by ubiquitin-mediated protein degradation." Chung C.Y., Reddy T.B.K., Zhou K., Firtel R.A. Genes Dev. 12:3564-3578(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INTERACTION WITH MKKA, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE. Strain: AX3.
[2]	"Sequence and analysis of chromosome 2 of Dictyostelium discoideum." Gloeckner G., Eichinger L., Szafranski K., Pachebat J.A., Bankier A.T., Dear P.H., Lehmann R., Baumgart C., Parra G., Abril J.F., Guigo R., Kumpf K., Tunggal B., Cox E.C., Quail M.A., Platzer M., Rosenthal A., Noegel A.A. Nature 418:79-85(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AX4.
[3]	"The genome of the social amoeba Dictyostelium discoideum." Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N. , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A. Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AX4.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF093690 mRNA. Translation: AAC97115.1. AAFI02000013 Genomic DNA. Translation: EAL69791.1. Different termination.
RefSeq	XP_643807.1. XM_638715.1.
3D structure databases
ProteinModelPortal	O96612.
ModBase	Search...
Protein-protein interaction databases
STRING	44689.DDB_0191402.
Protein family/group databases
MEROPS	C19.A68.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblProtists	DDB0191402; DDB0191402; DDB_G0275021.
GeneID	8619853.
KEGG	ddi:DDB_G0275021.
Organism-specific databases
dictyBase	DDB_G0275021. ubpB.
Phylogenomic databases
eggNOG	COG5560.
InParanoid	O96612.
KO	K11841.
OMA	INTSNTC.
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. False negative. PS00973. UCH_2_2. 1 hit. PS50235. UCH_2_3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

UBPB_DICDI

Accession

Primary (citable) accession number: O96612
Secondary accession number(s): Q554A4, Q869X4

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 24, 2009
Last sequence update:	May 1, 1999
Last modified:	May 29, 2013
This is version 61 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)