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Protein

OTU domain-containing protein 3

Gene

OTUD3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Deubiquitinating enzyme that hydrolyzes 'Lys-6'- and 'Lys-11'-linked polyubiquitin. Also hydrolyzes heterotypic (mixed and branched) and homotypic chains.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).1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei73 – 731By similarity
Active sitei76 – 761NucleophileBy similarity
Active sitei182 – 1821By similarity

GO - Molecular functioni

  1. ubiquitin-specific protease activity Source: UniProtKB

GO - Biological processi

  1. protein K11-linked deubiquitination Source: UniProtKB
  2. protein K6-linked deubiquitination Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Protein family/group databases

MEROPSiC85.003.

Names & Taxonomyi

Protein namesi
Recommended name:
OTU domain-containing protein 3 (EC:3.4.19.12)
Gene namesi
Name:OTUD3
Synonyms:KIAA0459
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:29038. OTUD3.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi178 – 1814RYGE → LSNG: Impaired activity. 1 Publication

Organism-specific databases

PharmGKBiPA142671215.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 398398OTU domain-containing protein 3PRO_0000058103Add
BLAST

Proteomic databases

MaxQBiQ5T2D3.
PaxDbiQ5T2D3.
PRIDEiQ5T2D3.

PTM databases

PhosphoSiteiQ5T2D3.

Expressioni

Gene expression databases

BgeeiQ5T2D3.
CleanExiHS_OTUD3.
ExpressionAtlasiQ5T2D3. baseline and differential.
GenevestigatoriQ5T2D3.

Organism-specific databases

HPAiHPA028543.
HPA028544.

Interactioni

Protein-protein interaction databases

BioGridi116856. 1 interaction.
STRINGi9606.ENSP00000364261.

Structurei

Secondary structure

1
398
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi56 – 627Combined sources
Beta strandi65 – 684Combined sources
Helixi76 – 8611Combined sources
Beta strandi87 – 893Combined sources
Helixi92 – 10514Combined sources
Helixi107 – 1104Combined sources
Helixi111 – 1133Combined sources
Helixi120 – 1289Combined sources
Helixi136 – 14510Combined sources
Beta strandi149 – 1535Combined sources
Beta strandi160 – 1667Combined sources
Beta strandi172 – 1787Combined sources
Turni179 – 1813Combined sources
Beta strandi182 – 1887Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4BOUX-ray1.55A52-209[»]
ProteinModelPortaliQ5T2D3.
SMRiQ5T2D3. Positions 52-190.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini65 – 189125OTUPROSITE-ProRule annotationAdd
BLAST
Domaini230 – 27041UBA-likeAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni70 – 767Cys-loop
Regioni127 – 13711Variable-loopAdd
BLAST
Regioni177 – 1826His-loop

Domaini

The UBA-like domain has no influence on ubiquitin hydrolysis.1 Publication
Specificity is given by the S1' ubiquitin-binding site within the OTU domain composed of the Cys-, His- and Variable-loops.1 Publication

Sequence similaritiesi

Contains 1 OTU domain.PROSITE-ProRule annotation
Contains 1 UBA-like domain.Curated

Phylogenomic databases

eggNOGiNOG136081.
GeneTreeiENSGT00390000016392.
HOGENOMiHOG000049263.
HOVERGENiHBG056738.
InParanoidiQ5T2D3.
KOiK13717.
OMAiQLPKVTN.
OrthoDBiEOG70ZZNW.
PhylomeDBiQ5T2D3.
TreeFamiTF329594.

Family and domain databases

InterProiIPR003323. OTU.
[Graphical view]
PfamiPF02338. OTU. 1 hit.
[Graphical view]
PROSITEiPS50802. OTU. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5T2D3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRKQAAKSR PGSGSRKAEA ERKRDERAAR RALAKERRNR PESGGGGGCE
60 70 80 90 100
EEFVSFANQL QALGLKLREV PGDGNCLFRA LGDQLEGHSR NHLKHRQETV
110 120 130 140 150
DYMIKQREDF EPFVEDDIPF EKHVASLAKP GTFAGNDAIV AFARNHQLNV
160 170 180 190 200
VIHQLNAPLW QIRGTEKSSV RELHIAYRYG EHYDSVRRIN DNSEAPAHLQ
210 220 230 240 250
TDFQMLHQDE SNKREKIKTK GMDSEDDLRD EVEDAVQKVC NATGCSDFNL
260 270 280 290 300
IVQNLEAENY NIESAIIAVL RMNQGKRNNA EENLEPSGRV LKQCGPLWEE
310 320 330 340 350
GGSGARIFGN QGLNEGRTEN NKAQASPSEE NKANKNQLAK VTNKQRREQQ
360 370 380 390
WMEKKKRQEE RHRHKALESR GSHRDNNRSE AEANTQVTLV KTFAALNI
Length:398
Mass (Da):45,124
Last modified:December 21, 2004 - v1
Checksum:i9C16E610CF1E3C5A
GO

Sequence cautioni

The sequence BAA32304.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti321 – 3211N → S.
Corresponds to variant rs2298110 [ dbSNP | Ensembl ].
VAR_051258
Natural varianti333 – 3331A → T.
Corresponds to variant rs10916668 [ dbSNP | Ensembl ].
VAR_051259

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB007928 mRNA. Translation: BAA32304.2. Different initiation.
AL391883 Genomic DNA. Translation: CAI17041.1.
CCDSiCCDS41279.1.
RefSeqiNP_056022.1. NM_015207.1.
UniGeneiHs.374987.

Genome annotation databases

EnsembliENST00000375120; ENSP00000364261; ENSG00000169914.
GeneIDi23252.
KEGGihsa:23252.
UCSCiuc001bcs.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB007928 mRNA. Translation: BAA32304.2. Different initiation.
AL391883 Genomic DNA. Translation: CAI17041.1.
CCDSiCCDS41279.1.
RefSeqiNP_056022.1. NM_015207.1.
UniGeneiHs.374987.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4BOUX-ray1.55A52-209[»]
ProteinModelPortaliQ5T2D3.
SMRiQ5T2D3. Positions 52-190.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116856. 1 interaction.
STRINGi9606.ENSP00000364261.

Protein family/group databases

MEROPSiC85.003.

PTM databases

PhosphoSiteiQ5T2D3.

Proteomic databases

MaxQBiQ5T2D3.
PaxDbiQ5T2D3.
PRIDEiQ5T2D3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000375120; ENSP00000364261; ENSG00000169914.
GeneIDi23252.
KEGGihsa:23252.
UCSCiuc001bcs.4. human.

Organism-specific databases

CTDi23252.
GeneCardsiGC01P020208.
HGNCiHGNC:29038. OTUD3.
HPAiHPA028543.
HPA028544.
MIMi611758. gene.
neXtProtiNX_Q5T2D3.
PharmGKBiPA142671215.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG136081.
GeneTreeiENSGT00390000016392.
HOGENOMiHOG000049263.
HOVERGENiHBG056738.
InParanoidiQ5T2D3.
KOiK13717.
OMAiQLPKVTN.
OrthoDBiEOG70ZZNW.
PhylomeDBiQ5T2D3.
TreeFamiTF329594.

Miscellaneous databases

GenomeRNAii23252.
NextBioi44955.
PROiQ5T2D3.
SOURCEiSearch...

Gene expression databases

BgeeiQ5T2D3.
CleanExiHS_OTUD3.
ExpressionAtlasiQ5T2D3. baseline and differential.
GenevestigatoriQ5T2D3.

Family and domain databases

InterProiIPR003323. OTU.
[Graphical view]
PfamiPF02338. OTU. 1 hit.
[Graphical view]
PROSITEiPS50802. OTU. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of cDNA clones in size-fractionated cDNA libraries from human brain."
    Seki N., Ohira M., Nagase T., Ishikawa K., Miyajima N., Nakajima D., Nomura N., Ohara O.
    DNA Res. 4:345-349(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain.
  2. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  4. "OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis."
    Mevissen T.E., Hospenthal M.K., Geurink P.P., Elliott P.R., Akutsu M., Arnaudo N., Ekkebus R., Kulathu Y., Wauer T., El Oualid F., Freund S.M., Ovaa H., Komander D.
    Cell 154:169-184(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF 52-209, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF 178-ARG--GLU-181.

Entry informationi

Entry nameiOTUD3_HUMAN
AccessioniPrimary (citable) accession number: Q5T2D3
Secondary accession number(s): O75047
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: December 21, 2004
Last modified: January 7, 2015
This is version 78 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.