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E1BY77

- UBP13_CHICK

UniProt

E1BY77 - UBP13_CHICK

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Protein
Ubiquitin carboxyl-terminal hydrolase 13
Gene
USP13
Organism
Gallus gallus (Chicken)
Status
Reviewed - Annotation score: 4 out of 5 - Protein inferred from homologyi

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 – 3401Nucleophile By similarity
Active sitei822 – 8221Proton acceptor By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri204 – 27673UBP-type
Add
BLAST

GO - Molecular functioni

  1. cysteine-type endopeptidase activity Source: UniProtKB
  2. omega peptidase activity Source: InterPro
  3. ubiquitin binding Source: UniProtKB
  4. ubiquitin thiolesterase activity Source: UniProtKB
  5. ubiquitin-specific protease 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
Complete GO annotation...

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 13
PRO_0000418012Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliE1BY77.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini331 – 860530USP
Add
BLAST
Domaini647 – 68842UBA 1
Add
BLAST
Domaini722 – 76241UBA 2
Add
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.
Contains 2 UBA domains.
Contains 1 USP domain.

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

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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: May 14, 2014
This is version 33 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

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