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Protein

Ubiquitin carboxyl-terminal hydrolase 33

Gene

usp33

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Deubiquitinating enzyme involved in various processes such as centrosome duplication, cellular migration and beta-2 adrenergic receptor/ADRB2 recycling. Involved in regulation of centrosome duplication by mediating deubiquitination of ccp110 in S and G2/M phase, leading to stabilize ccp110 during the period which centrioles duplicate and elongate. Involved in cell migration via its interaction with intracellular domain of robo1, leading to regulate the Slit signaling. Plays a role in commissural axon guidance cross the ventral midline of the neural tube in a Slit-dependent manner, possibly by mediating the deubiquitination of robo1. Acts as a regulator of G-protein coupled receptor (GPCR) signaling by mediating the deubiquitination of beta-arrestins (arrb1 and arrb2) and beta-2 adrenergic receptor (adrb2). Deubiquitinates dio2, thereby regulating thyroid hormone regulation. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains (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 sitei165 – 1651NucleophilePROSITE-ProRule annotation
Active sitei628 – 6281Proton acceptorPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri29 – 9365UBP-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. cysteine-type endopeptidase activity Source: UniProtKB
  2. ubiquitin-specific protease activity Source: UniProtKB
  3. zinc ion binding Source: UniProtKB

GO - Biological processi

  1. axon guidance Source: UniProtKB
  2. cell migration Source: UniProtKB
  3. centrosome duplication Source: UniProtKB
  4. endocytosis Source: UniProtKB-KW
  5. proteasome-mediated ubiquitin-dependent protein catabolic process Source: GO_Central
  6. protein deubiquitination Source: UniProtKB
  7. protein K48-linked deubiquitination Source: UniProtKB
  8. protein K63-linked deubiquitination Source: UniProtKB
  9. regulation of G-protein coupled receptor protein signaling pathway Source: UniProtKB
  10. regulation of proteasomal protein catabolic process Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Endocytosis, Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

Protein family/group databases

MEROPSiC19.037.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase 33 (EC:3.4.19.12)
Alternative name(s):
Deubiquitinating enzyme 33
Ubiquitin thioesterase 33
Ubiquitin-specific-processing protease 33
Gene namesi
Name:usp33
ORF Names:ch211-284g18.1
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437 Componenti: Chromosome 2

Organism-specific databases

ZFINiZDB-GENE-040426-2323. usp33.

Subcellular locationi

Cytoplasmperinuclear region By similarity. Cytoplasmcytoskeletonmicrotubule organizing centercentrosome By similarity
Note: Associates with centrosomes predominantly in S and G2 phases but less in G1 phase.By similarity

GO - Cellular componenti

  1. centrosome Source: UniProtKB
  2. perinuclear region of cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 897897Ubiquitin carboxyl-terminal hydrolase 33PRO_0000390426Add
BLAST

Expressioni

Gene expression databases

BgeeiA5PMR2.

Structurei

3D structure databases

ProteinModelPortaliA5PMR2.
SMRiA5PMR2. Positions 7-98.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini156 – 670515USPAdd
BLAST
Domaini672 – 76594DUSP 1PROSITE-ProRule annotationAdd
BLAST
Domaini773 – 876104DUSP 2PROSITE-ProRule annotationAdd
BLAST

Domaini

The UBP-type zinc finger binds 3 zinc ions. However, it does not bind ubiquitin, probably because the conserved Arg in position 55 is replaced by a Glu residue (By similarity).By similarity

Sequence similaritiesi

Contains 2 DUSP 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 fingeri29 – 9365UBP-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG5560.
GeneTreeiENSGT00780000121904.
HOGENOMiHOG000286031.
HOVERGENiHBG054196.
InParanoidiA5PMR2.
KOiK11848.
OMAiTMEEDKS.
OrthoDBiEOG7CRTP2.
PhylomeDBiA5PMR2.
TreeFamiTF352179.

Family and domain databases

Gene3Di3.30.2230.10. 2 hits.
3.30.40.10. 1 hit.
InterProiIPR006615. Pept_C19_DUSP.
IPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view]
PfamiPF06337. DUSP. 2 hits.
PF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
[Graphical view]
SMARTiSM00695. DUSP. 2 hits.
[Graphical view]
SUPFAMiSSF143791. SSF143791. 2 hits.
PROSITEiPS51283. DUSP. 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.

A5PMR2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGVSSNDCP HLECVGEITK EELIQKSHGQ CQDCKVGGPN LWACLENGCS
60 70 80 90 100
YVGCGESHAD HSTVHSQETR HNLTVNLTTL RVWCYACTKE VFLERKLGPH
110 120 130 140 150
KQLPNAAKAV SPVQTPCQDL NTPGSPTSLR VPSAGTCDDL DMETEEEDEL
160 170 180 190 200
RTRGLTGLKN IGNTCYMNAA LQALSNCPPL TQFFLECGGL VKTDKKPALC
210 220 230 240 250
KSYQKLITDL WHKNRNAYVV PTNLFQGIKA VNPMFRGYSQ QDSQEFLRCL
260 270 280 290 300
MDQLHEELKE LIPEPEDPNQ AVAMDDSPDE DNHSQSDDFQ SCESCGSSDR
310 320 330 340 350
ADNEGPRVPE DINEAEMLMP EQNQNNRDWQ KEKNLINNLY RAGSHGDLDK
360 370 380 390 400
DVDTTSDSRP IISSQGAIKA QGRTSDSEIQ VSSTVRPQSP TGNEGITSRL
410 420 430 440 450
SSSPPKSSAW PNLSSTHKKV PMFTPTKTKR QRKYHSIISE VFDGTIVSSV
460 470 480 490 500
QCLTCDRVSV TLENFQDISL PIPGKEDLAK LHSSSHQTAL VKAGSCGEAY
510 520 530 540 550
APQGWIAFVM EYIKSWFWGP VVTLQDCLAA FFARDELKGD NMYSCEKCKK
560 570 580 590 600
LRNGVKFCKV QSLPEILCIH LKRFRHELMF STKIGTHVSF PLEGLEMQPF
610 620 630 640 650
LAKDSSALTT TYDLLSVICH HGTASSGHYI AYCRNELNQL WYEFDDQSVT
660 670 680 690 700
EVSESCVQNA EAYVLFYKKS NDETQKERRK VTSLFNMMEP SLLQFYVSRQ
710 720 730 740 750
WLNKFKTFAE PGPISNHDFL CAHGGIPPNK AAYIDDLVLM IPQNVWDHLY
760 770 780 790 800
SRYGGGPAVN HLYVCHTCQN EIEKLEKRRK NELDMFVRLN KAFQEEESPV
810 820 830 840 850
VIYCISMQWF REWESFVKGK DIDPPGPIDN SKIAVNKNGH ITLKPGADSG
860 870 880 890
QISEETWNFL HNIHGGGPVV TVRPSVSHQE SETSQSEEKI EVETRTV
Length:897
Mass (Da):100,655
Last modified:July 9, 2007 - v1
Checksum:i19103583F04B4315
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti207 – 2071I → V in AAH66557 (Ref. 2) Curated
Sequence conflicti217 – 2171A → S in AAH66557 (Ref. 2) Curated
Sequence conflicti732 – 7321A → T in AAH66557 (Ref. 2) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX649634 Genomic DNA. Translation: CAN88027.1.
BC066557 mRNA. Translation: AAH66557.1.
RefSeqiNP_998392.1. NM_213227.1.
UniGeneiDr.32515.

Genome annotation databases

EnsembliENSDART00000018114; ENSDARP00000014516; ENSDARG00000016163.
GeneIDi406508.
KEGGidre:406508.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX649634 Genomic DNA. Translation: CAN88027.1.
BC066557 mRNA. Translation: AAH66557.1.
RefSeqiNP_998392.1. NM_213227.1.
UniGeneiDr.32515.

3D structure databases

ProteinModelPortaliA5PMR2.
SMRiA5PMR2. Positions 7-98.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiC19.037.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000018114; ENSDARP00000014516; ENSDARG00000016163.
GeneIDi406508.
KEGGidre:406508.

Organism-specific databases

CTDi23032.
ZFINiZDB-GENE-040426-2323. usp33.

Phylogenomic databases

eggNOGiCOG5560.
GeneTreeiENSGT00780000121904.
HOGENOMiHOG000286031.
HOVERGENiHBG054196.
InParanoidiA5PMR2.
KOiK11848.
OMAiTMEEDKS.
OrthoDBiEOG7CRTP2.
PhylomeDBiA5PMR2.
TreeFamiTF352179.

Miscellaneous databases

NextBioi20818084.
PROiA5PMR2.

Gene expression databases

BgeeiA5PMR2.

Family and domain databases

Gene3Di3.30.2230.10. 2 hits.
3.30.40.10. 1 hit.
InterProiIPR006615. Pept_C19_DUSP.
IPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view]
PfamiPF06337. DUSP. 2 hits.
PF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
[Graphical view]
SMARTiSM00695. DUSP. 2 hits.
[Graphical view]
SUPFAMiSSF143791. SSF143791. 2 hits.
PROSITEiPS51283. DUSP. 2 hits.
PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
PS50271. ZF_UBP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 496:498-503(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Tuebingen.
  2. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (JAN-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Embryo.

Entry informationi

Entry nameiUBP33_DANRE
AccessioniPrimary (citable) accession number: A5PMR2
Secondary accession number(s): Q6NYK6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 14, 2009
Last sequence update: July 9, 2007
Last modified: March 3, 2015
This is version 56 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

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.