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Protein

Ubiquitin thioesterase otubain-like

Gene

otub-1

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Hydrolase that can remove conjugated ubiquitin from proteins and plays an important regulatory role at the level of protein turnover by preventing degradation. Specifically cleaves 'Lys-48'-linked polyubiquitin.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).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei85 – 851By similarity
Active sitei88 – 881NucleophileBy similarity
Active sitei267 – 2671By similarity

GO - Molecular functioni

  1. ubiquitin-specific protease activity Source: WormBase

GO - Biological processi

  1. protein K48-linked deubiquitination Source: WormBase
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Protein family/group databases

MEROPSiC65.A01.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin thioesterase otubain-like (EC:3.4.19.12)
Alternative name(s):
Deubiquitinating enzyme otubain-like
Ubiquitin-specific-processing protease otubain-like
Gene namesi
Name:otub-1
ORF Names:C25D7.8
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
ProteomesiUP000001940 Componenti: Chromosome V

Organism-specific databases

WormBaseiC25D7.8; CE08394; WBGene00007718; otub-1.

Subcellular locationi

GO - Cellular componenti

  1. plasma membrane Source: WormBase
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 284284Ubiquitin thioesterase otubain-likePRO_0000221013Add
BLAST

Proteomic databases

PaxDbiQ9XVR6.

Interactioni

Protein-protein interaction databases

BioGridi533138. 2 interactions.
DIPiDIP-26135N.
IntActiQ9XVR6. 2 interactions.
MINTiMINT-1069399.
STRINGi6239.C25D7.8.

Structurei

Secondary structure

1
284
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi30 – 378Combined sources
Helixi38 – 403Combined sources
Helixi50 – 556Combined sources
Turni59 – 613Combined sources
Helixi63 – 7311Combined sources
Beta strandi76 – 805Combined sources
Helixi88 – 10316Combined sources
Helixi105 – 12420Combined sources
Helixi129 – 14719Combined sources
Beta strandi149 – 1513Combined sources
Helixi153 – 1619Combined sources
Helixi163 – 18321Combined sources
Helixi185 – 1884Combined sources
Helixi189 – 1913Combined sources
Helixi198 – 2058Combined sources
Helixi215 – 22410Combined sources
Beta strandi229 – 2357Combined sources
Helixi236 – 2383Combined sources
Beta strandi242 – 2498Combined sources
Beta strandi258 – 2647Combined sources
Beta strandi267 – 2737Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4DHIX-ray1.80B1-284[»]
4DHJX-ray2.35A/E/I/L1-284[»]
4DHZX-ray3.11A42-284[»]
4LDTX-ray1.90A42-284[»]
ProteinModelPortaliQ9XVR6.
SMRiQ9XVR6. Positions 28-275.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini77 – 274198OTUPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the peptidase C65 family.Curated
Contains 1 OTU domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG5539.
GeneTreeiENSGT00390000006979.
HOGENOMiHOG000019496.
InParanoidiQ9XVR6.
KOiK09602.
OMAiRVEYMDR.
PhylomeDBiQ9XVR6.

Family and domain databases

InterProiIPR003323. OTU.
IPR016615. Otubain.
IPR019400. Peptidase_C65_otubain.
[Graphical view]
PfamiPF10275. Peptidase_C65. 1 hit.
[Graphical view]
PIRSFiPIRSF013503. Ubiquitin_thioesterase_Otubain. 1 hit.
PROSITEiPS50802. OTU. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9XVR6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MANEPQKSDD NGQAAEAVVT DDEIVLQDQQ LKTIEDEQKS VPLVATLAPF
60 70 80 90 100
SILCAEYDNE TSAAFLSKAT ELSEVYGEIR YIRGDGNCFY RAILVGLIEI
110 120 130 140 150
MLKDRARLEK FIASSRDWTR TLVELGFPDW TCTDFCDFFI EFLEKIHSGV
160 170 180 190 200
HTEEAVYTIL NDDGSANYIL MFFRLITSAF LKQNSEEYAP FIDEGMTVAQ
210 220 230 240 250
YCEQEIEPMW KDADHLAINS LIKAAGTRVR IEYMDRTAAP NGGWHYDIPS
260 270 280
DDQQIAPEIT LLYRPGHYDV IYKKDSTEAS EIEN
Length:284
Mass (Da):32,293
Last modified:October 31, 1999 - v1
Checksum:i262500E41F8FA23C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z81039 Genomic DNA. Translation: CAB02772.1.
PIRiT19448.
RefSeqiNP_506709.1. NM_074308.4.
UniGeneiCel.4680.

Genome annotation databases

EnsemblMetazoaiC25D7.8; C25D7.8; WBGene00007718.
GeneIDi3565820.
KEGGicel:CELE_C25D7.8.
UCSCiC25D7.8. c. elegans.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z81039 Genomic DNA. Translation: CAB02772.1.
PIRiT19448.
RefSeqiNP_506709.1. NM_074308.4.
UniGeneiCel.4680.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4DHIX-ray1.80B1-284[»]
4DHJX-ray2.35A/E/I/L1-284[»]
4DHZX-ray3.11A42-284[»]
4LDTX-ray1.90A42-284[»]
ProteinModelPortaliQ9XVR6.
SMRiQ9XVR6. Positions 28-275.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi533138. 2 interactions.
DIPiDIP-26135N.
IntActiQ9XVR6. 2 interactions.
MINTiMINT-1069399.
STRINGi6239.C25D7.8.

Protein family/group databases

MEROPSiC65.A01.

Proteomic databases

PaxDbiQ9XVR6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiC25D7.8; C25D7.8; WBGene00007718.
GeneIDi3565820.
KEGGicel:CELE_C25D7.8.
UCSCiC25D7.8. c. elegans.

Organism-specific databases

CTDi3565820.
WormBaseiC25D7.8; CE08394; WBGene00007718; otub-1.

Phylogenomic databases

eggNOGiCOG5539.
GeneTreeiENSGT00390000006979.
HOGENOMiHOG000019496.
InParanoidiQ9XVR6.
KOiK09602.
OMAiRVEYMDR.
PhylomeDBiQ9XVR6.

Miscellaneous databases

NextBioi957977.
PROiQ9XVR6.

Family and domain databases

InterProiIPR003323. OTU.
IPR016615. Otubain.
IPR019400. Peptidase_C65_otubain.
[Graphical view]
PfamiPF10275. Peptidase_C65. 1 hit.
[Graphical view]
PIRSFiPIRSF013503. Ubiquitin_thioesterase_Otubain. 1 hit.
PROSITEiPS50802. OTU. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bristol N2.
  2. "Evidence for bidentate substrate binding as the basis for the K48 linkage specificity of otubain 1."
    Wang T., Yin L., Cooper E.M., Lai M.-Y., Dickey S., Pickart C.M., Fushman D., Wilkinson K.D., Cohen R.E., Wolberger C.
    J. Mol. Biol. 386:1011-1023(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiOTUBL_CAEEL
AccessioniPrimary (citable) accession number: Q9XVR6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 29, 2004
Last sequence update: October 31, 1999
Last modified: March 3, 2015
This is version 95 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Peptidase families
    Classification of peptidase families and list of entries
  4. 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.