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E1BY77

- UBP13_CHICK

UniProt

E1BY77 - UBP13_CHICK

Protein

Ubiquitin carboxyl-terminal hydrolase 13

Gene

USP13

Organism
Gallus gallus (Chicken)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 34 (01 Oct 2014)
      Sequence version 1 (02 Nov 2010)
      Previous versions | rss
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    Functioni

    Deubiquitinase that mediates deubiquitination of target proteins and is involved in various processes such as autophagy and endoplasmic reticulum-associated degradation (ERAD).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).

    Enzyme regulationi

    Specifically inhibited by spautin-1 (specific and potent autophagy inhibitor-1), a derivative of MBCQ that binds to USP13 and inhibits deubiquitinase activity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei340 – 3401NucleophilePROSITE-ProRule annotation
    Active sitei822 – 8221Proton acceptorPROSITE-ProRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri204 – 27673UBP-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. cysteine-type endopeptidase activity Source: UniProtKB
    2. omega peptidase activity Source: InterPro
    3. ubiquitin binding Source: UniProtKB
    4. ubiquitin-specific protease activity Source: UniProtKB
    5. ubiquitin thiolesterase activity Source: UniProtKB
    6. zinc ion binding Source: InterPro

    GO - Biological processi

    1. autophagy Source: UniProtKB-KW
    2. cell proliferation Source: UniProtKB
    3. protein K63-linked deubiquitination Source: UniProtKB
    4. protein stabilization Source: UniProtKB
    5. regulation of autophagy Source: UniProtKB
    6. regulation of transcription, DNA-templated Source: UniProtKB
    7. ubiquitin-dependent protein catabolic process Source: InterPro

    Keywords - Molecular functioni

    Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    Autophagy, Ubl conjugation pathway

    Keywords - Ligandi

    Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 13 (EC:3.4.19.12)
    Alternative name(s):
    Deubiquitinating enzyme 13
    Ubiquitin thioesterase 13
    Ubiquitin-specific-processing protease 13
    Gene namesi
    Name:USP13
    OrganismiGallus gallus (Chicken)
    Taxonomic identifieri9031 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiTestudines + Archosauria groupArchosauriaDinosauriaSaurischiaTheropodaCoelurosauriaAvesNeognathaeGalliformesPhasianidaePhasianinaeGallus
    ProteomesiUP000000539: Chromosome 9

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 862862Ubiquitin carboxyl-terminal hydrolase 13PRO_0000418012Add
    BLAST

    Structurei

    3D structure databases

    ProteinModelPortaliE1BY77.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini331 – 860530USPAdd
    BLAST
    Domaini647 – 68842UBA 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini722 – 76241UBA 2PROSITE-ProRule annotationAdd
    BLAST

    Domaini

    The UBP-type zinc finger has lost its ability to bind ubiquitin and USP13 is not activated by unanchored ubiquitin.By similarity
    The UBA domains mediate binding to ubiquitin.By similarity

    Sequence similaritiesi

    Belongs to the peptidase C19 family.Curated
    Contains 2 UBA domains.PROSITE-ProRule annotation
    Contains 1 UBP-type zinc finger.PROSITE-ProRule annotation
    Contains 1 USP domain.Curated

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri204 – 27673UBP-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    GeneTreeiENSGT00390000000874.
    KOiK11836.
    OMAiPRMFKAF.
    OrthoDBiEOG7CNZF3.
    PhylomeDBiE1BY77.
    TreeFamiTF300576.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR009060. UBA-like.
    IPR015940. UBA/transl_elong_EF1B_N_euk.
    IPR000449. UBA/Ts_N.
    IPR016652. Ubiquitinyl_hydrolase.
    IPR028889. UCH/PAN2.
    IPR013083. Znf_RING/FYVE/PHD.
    IPR001607. Znf_UBP.
    [Graphical view]
    PfamiPF00627. UBA. 2 hits.
    PF00443. UCH. 1 hit.
    PF02148. zf-UBP. 1 hit.
    [Graphical view]
    PIRSFiPIRSF016308. UBP. 1 hit.
    SMARTiSM00165. UBA. 2 hits.
    SM00290. ZnF_UBP. 1 hit.
    [Graphical view]
    SUPFAMiSSF46934. SSF46934. 1 hit.
    PROSITEiPS50030. UBA. 2 hits.
    PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    PS50271. ZF_UBP. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    E1BY77-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQRAALFGGG DAQMAAGDLG ELLVPYMPTI RVPKSGDRVY KTECAFSYDS    50
    PDSEGGLYVC MNTFLGFGRE HIERHYRKTG QCVYLHLKRH VIEKVPGASG 100
    GALPKRRNAK LFLDLEANGD LSSDDFEYED EAKLVIFPDH YEISLPNIEE 150
    LPALVTIASD ALLSAKSPYR KQDPDSWEEE LQASKHAKSL VQLDNGVRIP 200
    PSGWKCSKCD LRENLWLNLT DGSVLCGKWF FDGSGGNGHA MEHYKETGYP 250
    LAVKLGTITP DGADVYSFDE EEPVLDPHIA KHLAHFGIDM LQMQVAENGL 300
    RDNDIKPRVS EWEVIQEAGV KLKPMYGPGY TGMKNLGNSC YLNAVMQAIF 350
    SIPEFQRAYV GNLPRIFDYS PLDPTQDFNT QMAKLGHGLL SGQYSKPPMK 400
    SELIEQVMKE EHKPQQNGIS PQMFKAFISK DHTEFSSNRQ QDAQEFFLHL 450
    INLVERNPVG SENPSDVFRF LVEERTQCCQ SRKVRYTERV DYIMQLPVAM 500
    EAATNKDELI AYELKRREAE AARRAPPELV RAKIPFSACL QAFSEPTNVE 550
    DFWSSALQAK SAGVKTSRFA SFPQYLVVQI KKFTFGLDWI PKKLDVSIDM 600
    PDFLDISHLR AMGLQPGEEE LPDIAPPIII PEDPKDRMMN NFVESLDIDE 650
    SSVMQLAEMG FPLEACRKAV YYTGNLGAEV AFNWIIAHME EPDFAEPLVV 700
    PVFGGAASSG VAGLGAVGLD NQPPEEMVSI IISMGFQRSL AIQALKATNN 750
    NLERALEWIF SHPELEEEDG EPALNVMDLE NHTNANILAE ARSEGPRIKD 800
    GPGRYELFGF ISHMGTSTMS GHYVCHLKKE GRWVIYNDLR VCASERPPKD 850
    LGYIYFYHRI PS 862
    Length:862
    Mass (Da):96,649
    Last modified:November 2, 2010 - v1
    Checksum:i9207A3B6846A1018
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AADN02020803 Genomic DNA. No translation available.
    AADN02020804 Genomic DNA. No translation available.
    AADN02020805 Genomic DNA. No translation available.
    AADN02020806 Genomic DNA. No translation available.
    RefSeqiXP_426842.2. XM_426842.4.

    Genome annotation databases

    EnsembliENSGALT00000014487; ENSGALP00000014471; ENSGALG00000008909.
    GeneIDi429286.
    KEGGigga:429286.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AADN02020803 Genomic DNA. No translation available.
    AADN02020804 Genomic DNA. No translation available.
    AADN02020805 Genomic DNA. No translation available.
    AADN02020806 Genomic DNA. No translation available.
    RefSeqi XP_426842.2. XM_426842.4.

    3D structure databases

    ProteinModelPortali E1BY77.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSGALT00000014487 ; ENSGALP00000014471 ; ENSGALG00000008909 .
    GeneIDi 429286.
    KEGGi gga:429286.

    Organism-specific databases

    CTDi 8975.

    Phylogenomic databases

    GeneTreei ENSGT00390000000874.
    KOi K11836.
    OMAi PRMFKAF.
    OrthoDBi EOG7CNZF3.
    PhylomeDBi E1BY77.
    TreeFami TF300576.

    Miscellaneous databases

    NextBioi 20830031.
    PROi E1BY77.

    Family and domain databases

    Gene3Di 3.30.40.10. 1 hit.
    InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR009060. UBA-like.
    IPR015940. UBA/transl_elong_EF1B_N_euk.
    IPR000449. UBA/Ts_N.
    IPR016652. Ubiquitinyl_hydrolase.
    IPR028889. UCH/PAN2.
    IPR013083. Znf_RING/FYVE/PHD.
    IPR001607. Znf_UBP.
    [Graphical view ]
    Pfami PF00627. UBA. 2 hits.
    PF00443. UCH. 1 hit.
    PF02148. zf-UBP. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF016308. UBP. 1 hit.
    SMARTi SM00165. UBA. 2 hits.
    SM00290. ZnF_UBP. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46934. SSF46934. 1 hit.
    PROSITEi PS50030. UBA. 2 hits.
    PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    PS50271. ZF_UBP. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution."
      Hillier L.W., Miller W., Birney E., Warren W., Hardison R.C., Ponting C.P., Bork P., Burt D.W., Groenen M.A.M., Delany M.E., Dodgson J.B., Chinwalla A.T., Cliften P.F., Clifton S.W., Delehaunty K.D., Fronick C., Fulton R.S., Graves T.A.
      , Kremitzki C., Layman D., Magrini V., McPherson J.D., Miner T.L., Minx P., Nash W.E., Nhan M.N., Nelson J.O., Oddy L.G., Pohl C.S., Randall-Maher J., Smith S.M., Wallis J.W., Yang S.-P., Romanov M.N., Rondelli C.M., Paton B., Smith J., Morrice D., Daniels L., Tempest H.G., Robertson L., Masabanda J.S., Griffin D.K., Vignal A., Fillon V., Jacobbson L., Kerje S., Andersson L., Crooijmans R.P., Aerts J., van der Poel J.J., Ellegren H., Caldwell R.B., Hubbard S.J., Grafham D.V., Kierzek A.M., McLaren S.R., Overton I.M., Arakawa H., Beattie K.J., Bezzubov Y., Boardman P.E., Bonfield J.K., Croning M.D.R., Davies R.M., Francis M.D., Humphray S.J., Scott C.E., Taylor R.G., Tickle C., Brown W.R.A., Rogers J., Buerstedde J.-M., Wilson S.A., Stubbs L., Ovcharenko I., Gordon L., Lucas S., Miller M.M., Inoko H., Shiina T., Kaufman J., Salomonsen J., Skjoedt K., Wong G.K.-S., Wang J., Liu B., Wang J., Yu J., Yang H., Nefedov M., Koriabine M., Dejong P.J., Goodstadt L., Webber C., Dickens N.J., Letunic I., Suyama M., Torrents D., von Mering C., Zdobnov E.M., Makova K., Nekrutenko A., Elnitski L., Eswara P., King D.C., Yang S.-P., Tyekucheva S., Radakrishnan A., Harris R.S., Chiaromonte F., Taylor J., He J., Rijnkels M., Griffiths-Jones S., Ureta-Vidal A., Hoffman M.M., Severin J., Searle S.M.J., Law A.S., Speed D., Waddington D., Cheng Z., Tuzun E., Eichler E., Bao Z., Flicek P., Shteynberg D.D., Brent M.R., Bye J.M., Huckle E.J., Chatterji S., Dewey C., Pachter L., Kouranov A., Mourelatos Z., Hatzigeorgiou A.G., Paterson A.H., Ivarie R., Brandstrom M., Axelsson E., Backstrom N., Berlin S., Webster M.T., Pourquie O., Reymond A., Ucla C., Antonarakis S.E., Long M., Emerson J.J., Betran E., Dupanloup I., Kaessmann H., Hinrichs A.S., Bejerano G., Furey T.S., Harte R.A., Raney B., Siepel A., Kent W.J., Haussler D., Eyras E., Castelo R., Abril J.F., Castellano S., Camara F., Parra G., Guigo R., Bourque G., Tesler G., Pevzner P.A., Smit A., Fulton L.A., Mardis E.R., Wilson R.K.
      Nature 432:695-716(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Red jungle fowl.

    Entry informationi

    Entry nameiUBP13_CHICK
    AccessioniPrimary (citable) accession number: E1BY77
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 13, 2012
    Last sequence update: November 2, 2010
    Last modified: October 1, 2014
    This is version 34 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

    Complete proteome, Reference proteome

    Documents

    1. Peptidase families
      Classification of peptidase families and list of entries
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3