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Protein

Probable ubiquitin carboxyl-terminal hydrolase 4

Gene

ubp4

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Has an ATP-independent isopeptidase activity, cleaving at the C-terminus of the ubiquitin moiety. Acts late in the proteolytic pathway in conjunction with the 26S proteasome. Plays a role in avoiding DNA overreplication (By similarity).By similarity

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).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei236 – 2361NucleophilePROSITE-ProRule annotation
Active sitei530 – 5301Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

  • cysteine-type endopeptidase activity Source: GO_Central
  • ubiquitin-specific protease activity Source: PomBase

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Enzyme and pathway databases

ReactomeiREACT_362021. Termination of translesion DNA synthesis.

Protein family/group databases

MEROPSiC19.A58.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable ubiquitin carboxyl-terminal hydrolase 4 (EC:3.4.19.12)
Alternative name(s):
Deubiquitinating enzyme 4
Ubiquitin thioesterase 4
Ubiquitin-specific-processing protease 4
Gene namesi
Name:ubp4
ORF Names:SPBC18H10.08c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
ProteomesiUP000002485 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:SPBC18H10.08c.
PomBaseiSPBC18H10.08c. ubp4.

Subcellular locationi

GO - Cellular componenti

  • cell division site Source: PomBase
  • cytoplasm Source: PomBase
  • endosome Source: PomBase
  • transport vesicle Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 593593Probable ubiquitin carboxyl-terminal hydrolase 4PRO_0000080605Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei338 – 3381Phosphoserine1 Publication
Modified residuei343 – 3431Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiO60139.

Interactioni

Subunit structurei

Interacts with sfp47.1 Publication

Protein-protein interaction databases

BioGridi277355. 91 interactions.
MINTiMINT-4677554.
STRINGi4896.SPBC18H10.08c.1.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini227 – 573347USPAdd
BLAST

Sequence similaritiesi

Belongs to the peptidase C19 family.Curated
Contains 1 USP domain.Curated

Phylogenomic databases

eggNOGiCOG5533.
InParanoidiO60139.
KOiK11839.
OrthoDBiEOG7R2BSX.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
[Graphical view]
PfamiPF00443. UCH. 1 hit.
[Graphical view]
PROSITEiPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O60139-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDDYFDRLF ELAFVYINED ETIQSCSFRG QRWLEEAQTL EQKNSLLKAY
60 70 80 90 100
YYYLKALKLA YEIPCRFEIS VKSTHYGEFK QFQKLAIQAV SKAFTIKSKL
110 120 130 140 150
AVKHYLPVIQ ISDALSLSKK SSLKVLFLNF YSQESSKGYV FSKHTIAIPI
160 170 180 190 200
SCLQSMDSSK IYDFLKSAPF HPSMVICYSL ERYFEDVSLA YKLYSMLRSL
210 220 230 240 250
KLDPHFMELA NPKKVDSSLS YENYQPIGLT NLGNTCYMNC VLQCLFACKD
260 270 280 290 300
LTIPMLQGRG LLQNINTKNP LGTGGKITSA FFSLLQSVLL NHGQRSISPR
310 320 330 340 350
NFLEIVQSLN RDFSIDGQCD AQEFLNFFLD KLHEDLNSNA SRSPIAPLTE
360 370 380 390 400
DQLSAREELP LSHFSHIEWN LHLRSNKSIV VNNFVGQLCS RTQCMTCGRT
410 420 430 440 450
STTFAPFTSL AIPIDDVSHV VSLQECLLKF SAPELLQGHD GWHCPVCKVQ
460 470 480 490 500
RSAKKVIMIS KLPEYLIIQI QRFKISVMGR KKIDTPLGLS LQIPSKMLVP
510 520 530 540 550
PSFQSGIGYI PSNYNLFAFI CHYGQLENGH YISDVLFNNE WCHIDDSIVR
560 570 580 590
TVGGITDLRE DFSSSYILFY KRSSLLEEFE DKCPKMTLKR NVK
Length:593
Mass (Da):67,747
Last modified:April 18, 2012 - v2
Checksum:i16801C84BB258B61
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329671 Genomic DNA. Translation: CAA18405.2.
PIRiT39772.
RefSeqiNP_595732.2. NM_001021630.2.

Genome annotation databases

EnsemblFungiiSPBC18H10.08c.1; SPBC18H10.08c.1:pep; SPBC18H10.08c.
GeneIDi2540837.
KEGGispo:SPBC18H10.08c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329671 Genomic DNA. Translation: CAA18405.2.
PIRiT39772.
RefSeqiNP_595732.2. NM_001021630.2.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi277355. 91 interactions.
MINTiMINT-4677554.
STRINGi4896.SPBC18H10.08c.1.

Protein family/group databases

MEROPSiC19.A58.

Proteomic databases

MaxQBiO60139.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPBC18H10.08c.1; SPBC18H10.08c.1:pep; SPBC18H10.08c.
GeneIDi2540837.
KEGGispo:SPBC18H10.08c.

Organism-specific databases

EuPathDBiFungiDB:SPBC18H10.08c.
PomBaseiSPBC18H10.08c. ubp4.

Phylogenomic databases

eggNOGiCOG5533.
InParanoidiO60139.
KOiK11839.
OrthoDBiEOG7R2BSX.

Enzyme and pathway databases

ReactomeiREACT_362021. Termination of translesion DNA synthesis.

Miscellaneous databases

NextBioi20801954.
PROiO60139.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
[Graphical view]
PfamiPF00443. UCH. 1 hit.
[Graphical view]
PROSITEiPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  2. "ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe."
    Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S., Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S., Yoshida M.
    Nat. Biotechnol. 24:841-847(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  3. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-338 AND SER-343, IDENTIFICATION BY MASS SPECTROMETRY.
  4. "A global census of fission yeast deubiquitinating enzyme localization and interaction networks reveals distinct compartmentalization profiles and overlapping functions in endocytosis and polarity."
    Kouranti I., McLean J.R., Feoktistova A., Liang P., Johnson A.E., Roberts-Galbraith R.H., Gould K.L.
    PLoS Biol. 8:708-716(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SFP47, SUBCELLULAR LOCATION.
  5. "Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability."
    Bitton D.A., Wood V., Scutt P.J., Grallert A., Yates T., Smith D.L., Hagan I.M., Miller C.J.
    Genetics 187:1207-1217(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVISION OF GENE MODEL.

Entry informationi

Entry nameiUBP4_SCHPO
AccessioniPrimary (citable) accession number: O60139
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 2002
Last sequence update: April 18, 2012
Last modified: June 24, 2015
This is version 104 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  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.