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Q8CB27

- OTU1_MOUSE

UniProt

Q8CB27 - OTU1_MOUSE

Protein

Ubiquitin thioesterase OTU1

Gene

Yod1

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 96 (01 Oct 2014)
      Sequence version 1 (01 Mar 2003)
      Previous versions | rss
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    Functioni

    Hydrolase that can remove conjugated ubiquitin from proteins and participates in endoplasmic reticulum-associated degradation (ERAD) for misfolded lumenal proteins. May act by triming the ubiquitin chain on the associated substrate to facilitate their threading through the VCP/p97 pore. Ubiquitin moieties on substrates may present a steric impediment to the threading process when the substrate is transferred to the VCP pore and threaded through VCP's axial channel. Mediates deubiquitination of 'Lys-27'-, 'Lys-29'- and 'Lys-33'-linked polyubiquitin chains. Also able to hydrolyze 'Lys-11'-linked ubiquitin chains. Cleaves both polyubiquitin and di-ubiquitin 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 sitei152 – 1521By similarity
    Active sitei155 – 1551NucleophileBy similarity
    Binding sitei261 – 2611Substrate; via carbonyl oxygenBy similarity
    Active sitei262 – 2621By similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri313 – 33725C2H2-typeAdd
    BLAST

    GO - Molecular functioni

    1. metal ion binding Source: UniProtKB-KW
    2. ubiquitin-specific protease activity Source: UniProtKB

    GO - Biological processi

    1. cellular amino acid metabolic process Source: UniProtKB
    2. endoplasmic reticulum unfolded protein response Source: UniProtKB
    3. ER-associated ubiquitin-dependent protein catabolic process Source: UniProtKB
    4. protein K11-linked deubiquitination Source: UniProtKB
    5. protein K27-linked deubiquitination Source: UniProtKB
    6. protein K29-linked deubiquitination Source: UniProtKB
    7. protein K33-linked deubiquitination Source: UniProtKB
    8. protein K48-linked deubiquitination Source: UniProtKB
    9. protein K63-linked deubiquitination Source: UniProtKB

    Keywords - Molecular functioni

    Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    Ubl conjugation pathway, Unfolded protein response

    Keywords - Ligandi

    Metal-binding, Zinc

    Protein family/group databases

    MEROPSiC85.007.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin thioesterase OTU1 (EC:3.4.19.12)
    Gene namesi
    Name:Yod1
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 1

    Organism-specific databases

    MGIiMGI:2442596. Yod1.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 343343Ubiquitin thioesterase OTU1PRO_0000282357Add
    BLAST

    Proteomic databases

    PaxDbiQ8CB27.
    PRIDEiQ8CB27.

    PTM databases

    PhosphoSiteiQ8CB27.

    Expressioni

    Gene expression databases

    BgeeiQ8CB27.
    GenevestigatoriQ8CB27.

    Interactioni

    Subunit structurei

    Interacts with VCP; the interaction is direct. Interacts with FAF2/UBXD8. Interacts with DERL1; however interaction is dependent on the UBAX-like region, suggesting that it may be indirect By similarity.By similarity

    Protein-protein interaction databases

    STRINGi10090.ENSMUSP00000055318.

    Structurei

    Secondary structure

    1
    343
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi44 – 485
    Beta strandi51 – 555
    Helixi64 – 7411
    Turni79 – 813
    Beta strandi85 – 884
    Turni102 – 1043
    Beta strandi112 – 1143

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2KZRNMR-A42-126[»]
    ProteinModelPortaliQ8CB27.
    SMRiQ8CB27. Positions 42-127, 142-306.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini144 – 269126OTUPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni45 – 12379UBX-likeAdd
    BLAST
    Regioni149 – 1557Cys-loopBy similarity
    Regioni208 – 21811Variable-loopBy similarityAdd
    BLAST
    Regioni258 – 2625His-loopBy similarity
    Regioni286 – 2916S2 siteBy similarity

    Domaini

    The UBAX-like region mediates the interaction with VCP.By similarity
    The C2H2-type zinc finger mediates specificity for 'Lys-27'-, 'Lys-29'- and 'Lys-33'-linked polyubiquitin chains but not for 'Lys-11'-linked ubiquitin chains. Selectivity for 'Lys-11'-linked ubiquitin chains is provided by recognition of the sequence surrounding 'Lys-11' in ubiquitin. The S2 site region provides specificity for longer 'Lys-11'-linked ubiquitin chains By similarity.By similarity

    Sequence similaritiesi

    Contains 1 C2H2-type zinc finger.Curated
    Contains 1 OTU domain.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri313 – 33725C2H2-typeAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiCOG5539.
    GeneTreeiENSGT00390000009989.
    HOGENOMiHOG000193461.
    HOVERGENiHBG097006.
    InParanoidiB2RSW9.
    KOiK13719.
    OMAiKSSRQFT.
    OrthoDBiEOG7J1808.
    PhylomeDBiQ8CB27.
    TreeFamiTF323700.

    Family and domain databases

    InterProiIPR003323. OTU.
    IPR029071. Ubiquitin-rel_dom.
    IPR007087. Znf_C2H2.
    IPR015880. Znf_C2H2-like.
    [Graphical view]
    PfamiPF02338. OTU. 1 hit.
    [Graphical view]
    SMARTiSM00355. ZnF_C2H2. 1 hit.
    [Graphical view]
    SUPFAMiSSF54236. SSF54236. 1 hit.
    PROSITEiPS50802. OTU. 1 hit.
    PS00028. ZINC_FINGER_C2H2_1. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q8CB27-1 [UniParc]FASTAAdd to Basket

    « Hide

    MFGGAKGGHF GVPPAGYSGA VPQSEAGTKA GPAGGRPADT MWRVRCKAKG    50
    GTHLLQGLSS RTRLRELQGQ IAAITGIAPG SQRILVGYPP ECLDLSDRDI 100
    TLGDLPIQSG DMLIVEEDQT RPKASPAFSK YGAPSYVREA LPVLTRTAVP 150
    ADNSCLFTSV YYVVEGGVLN PACAPEMRRL IAQIVASDPV LYSEAILGKT 200
    NEDYCDWIRR DDTWGGAIEI SILSKFYQCE ICVVDTQTVR IDRFGEDAGY 250
    TKRVLLIYDG IHYDPLQRNF PDPDTPPLTI FSSNDDIVLV QALELADEAR 300
    RKRQFTDVNR FTLRCMICQK GLTGQAEARD HARETGHTNF GEV 343
    Length:343
    Mass (Da):37,485
    Last modified:March 1, 2003 - v1
    Checksum:iC07F3F69F1CA86D8
    GO

    Sequence cautioni

    The sequence BAC29661.1 differs from that shown. Reason: Frameshift at position 8.
    The sequence BAC35495.1 differs from that shown. Reason: Erroneous termination at position 344. Translated as stop.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK036938 mRNA. Translation: BAC29646.1.
    AK036991 mRNA. Translation: BAC29661.1. Frameshift.
    AK053730 mRNA. Translation: BAC35495.1. Sequence problems.
    BC139034 mRNA. Translation: AAI39035.1.
    CCDSiCCDS48351.1.
    RefSeqiNP_848806.2. NM_178691.4.
    UniGeneiMm.106553.

    Genome annotation databases

    EnsembliENSMUST00000049813; ENSMUSP00000055318; ENSMUSG00000046404.
    GeneIDi226418.
    KEGGimmu:226418.
    UCSCiuc007cmh.2. mouse.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK036938 mRNA. Translation: BAC29646.1 .
    AK036991 mRNA. Translation: BAC29661.1 . Frameshift.
    AK053730 mRNA. Translation: BAC35495.1 . Sequence problems.
    BC139034 mRNA. Translation: AAI39035.1 .
    CCDSi CCDS48351.1.
    RefSeqi NP_848806.2. NM_178691.4.
    UniGenei Mm.106553.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2KZR NMR - A 42-126 [» ]
    ProteinModelPortali Q8CB27.
    SMRi Q8CB27. Positions 42-127, 142-306.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 10090.ENSMUSP00000055318.

    Protein family/group databases

    MEROPSi C85.007.

    PTM databases

    PhosphoSitei Q8CB27.

    Proteomic databases

    PaxDbi Q8CB27.
    PRIDEi Q8CB27.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000049813 ; ENSMUSP00000055318 ; ENSMUSG00000046404 .
    GeneIDi 226418.
    KEGGi mmu:226418.
    UCSCi uc007cmh.2. mouse.

    Organism-specific databases

    CTDi 55432.
    MGIi MGI:2442596. Yod1.

    Phylogenomic databases

    eggNOGi COG5539.
    GeneTreei ENSGT00390000009989.
    HOGENOMi HOG000193461.
    HOVERGENi HBG097006.
    InParanoidi B2RSW9.
    KOi K13719.
    OMAi KSSRQFT.
    OrthoDBi EOG7J1808.
    PhylomeDBi Q8CB27.
    TreeFami TF323700.

    Miscellaneous databases

    NextBioi 378144.
    PROi Q8CB27.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q8CB27.
    Genevestigatori Q8CB27.

    Family and domain databases

    InterProi IPR003323. OTU.
    IPR029071. Ubiquitin-rel_dom.
    IPR007087. Znf_C2H2.
    IPR015880. Znf_C2H2-like.
    [Graphical view ]
    Pfami PF02338. OTU. 1 hit.
    [Graphical view ]
    SMARTi SM00355. ZnF_C2H2. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54236. SSF54236. 1 hit.
    PROSITEi PS50802. OTU. 1 hit.
    PS00028. ZINC_FINGER_C2H2_1. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: C57BL/6J.
      Tissue: Eye and Vagina.
    2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Brain.
    3. "Northeast structural genomics consortium target mmt2a."
      Northeast structural genomics consortium (NESG)
      Submitted (AUG-2010) to the PDB data bank
      Cited for: STRUCTURE BY NMR OF 42-126.

    Entry informationi

    Entry nameiOTU1_MOUSE
    AccessioniPrimary (citable) accession number: Q8CB27
    Secondary accession number(s): B2RSW9, Q8BPM9, Q8CB24
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 3, 2007
    Last sequence update: March 1, 2003
    Last modified: October 1, 2014
    This is version 96 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3