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A8HAL1

- UBP16_DANRE

UniProt

A8HAL1 - UBP16_DANRE

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Protein
Ubiquitin carboxyl-terminal hydrolase 16
Gene
usp16, si:dkey-121n8.2
Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 5 out of 5 - Protein inferred from homologyi

Functioni

Specifically deubiquitinates 'Lys-120' of histone H2A (H2AK119Ub), a specific tag for epigenetic transcriptional repression, thereby acting as a coactivator. Deubiquitination of histone H2A is a prerequisite for subsequent phosphorylation at 'Ser-11' of histone H3 (H3S10ph), and is required for chromosome segregation when cells enter into mitosis. Regulates Hox gene expression via histone H2A deubiquitination. Prefers nucleosomal substrates. Does not deubiquitinate histone H2B By similarity.UniRule annotation

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).UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi24 – 241Zinc 1 By similarity
Metal bindingi26 – 261Zinc 1 By similarity
Metal bindingi48 – 481Zinc 2 By similarity
Metal bindingi51 – 511Zinc 2 By similarity
Metal bindingi76 – 761Zinc 3 By similarity
Metal bindingi79 – 791Zinc 3 By similarity
Metal bindingi84 – 841Zinc 2 By similarity
Metal bindingi91 – 911Zinc 2 By similarity
Metal bindingi95 – 951Zinc 3 By similarity
Metal bindingi104 – 1041Zinc 3 By similarity
Metal bindingi117 – 1171Zinc 1 By similarity
Metal bindingi120 – 1201Zinc 1 By similarity
Active sitei217 – 2171Nucleophile By similarity
Active sitei752 – 7521Proton acceptor By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri46 – 12681UBP-typeUniRule annotation
Add
BLAST

GO - Molecular functioni

  1. cysteine-type endopeptidase activity Source: UniProtKB
  2. histone binding Source: UniProtKB
  3. transcription coactivator activity Source: UniProtKB
  4. ubiquitin binding Source: UniProtKB
  5. ubiquitin thiolesterase activity Source: UniProtKB
  6. ubiquitin-specific protease activity Source: UniProtKB
  7. zinc ion binding Source: UniProtKB
Complete GO annotation...

GO - Biological processi

  1. cellular response to DNA damage stimulus Source: UniProtKB
  2. histone H2A K63-linked deubiquitination Source: UniProtKB
  3. histone deubiquitination Source: UniProtKB
  4. mitotic nuclear division Source: UniProtKB
  5. positive regulation of transcription, DNA-templated Source: UniProtKB
  6. positive regulation of translational elongation Source: UniProtKB
  7. protein homotetramerization Source: UniProtKB
  8. transcription, DNA-templated Source: UniProtKB-KW
  9. ubiquitin-dependent protein catabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Activator, Chromatin regulator, Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Cell cycle, Cell division, Mitosis, Transcription, Transcription regulation, Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase 16 (EC:3.4.19.12)
Alternative name(s):
Deubiquitinating enzyme 16
Ubiquitin thioesterase 16
Ubiquitin-specific-processing protease 16
Gene namesi
Name:usp16
ORF Names:si:dkey-121n8.2
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437: Chromosome 15

Subcellular locationi

Nucleus By similarity UniRule annotation

GO - Cellular componenti

  1. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 815815Ubiquitin carboxyl-terminal hydrolase 16UniRule annotation
PRO_0000367505Add
BLAST

Expressioni

Gene expression databases

BgeeiA8HAL1.

Interactioni

Subunit structurei

Homotetramer By similarity.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliA8HAL1.
SMRiA8HAL1. Positions 22-142.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini208 – 814607USP
Add
BLAST

Domaini

The UBP-type zinc finger binds 3 zinc ions that form a pair of cross-braced ring fingers encapsulated within a third zinc finger in the primary structure. It recognizes the C-terminal tail of free ubiquitin By similarity.UniRule annotation

Sequence similaritiesi

Contains 1 USP domain.

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG5560.
GeneTreeiENSGT00750000117419.
HOGENOMiHOG000154755.
HOVERGENiHBG062704.
KOiK11844.
OMAiECSIQHC.
OrthoDBiEOG7J9VNZ.
PhylomeDBiA8HAL1.
TreeFamiTF326075.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
HAMAPiMF_03062. UBP16.
InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view]
PfamiPF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
[Graphical view]
PROSITEiPS00972. 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.

A8HAL1-1 [UniParc]FASTAAdd to Basket

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MGKKKVKDRS AGTDSSSETA GPSCTHIRKG TENSVLKKAC LNEHWSSCQD    50
CEQDKPEEKQ ILEDQTDGES PAVWMCLKCG HRGCGRSGNQ HAIKHYETPR 100
SEPHCLVLSL DVWSVWCYIC DDEVQYSSTG QLAQLITNIR KQVLTAPDKR 150
NASKKSWKED ISVMNSAEQT QDEEKGKKGK QKSSSKQEDS PKSHQSAAAG 200
SSAVVSVRGL SNLGNTCFFN AVVQSLSQTQ YLRELLKQIA EEKSSFSITP 250
ALSSELDPLQ IQLERPGSLT LAMCQLMNEI QETKKGVVTP KELFTQVCKK 300
APRFKGFQQQ DSQELLRYLL DGMRAEEAKR VNSGILEALK SSGKNFEAEQ 350
TKKIVKEYEK DGAPKNFVDR VFGGAMSSTV MCKECKTVSL VTEMFLDLSL 400
PVADEAYRKK NQKKAVQHRH SVSDDGDQDT SSLANGNEDM PTGTGSKYQQ 450
KKAKKQAKKQ AKNQRRQQKQ GGKVTLDAIT NQSSTDPADS SMQTQTVSVN 500
GSADAQPADT NQEDLSLEKH NEDQDDEEPE QEQAASVNNR FTALSEDQTT 550
EDIAEQVNED EDEIEQNCAE EEELVEELNT MSLTTPSEGD VENGEDTLED 600
VKEYTVVNRD PELAFRALAS RTAPVKQECS VESCLYQFTE VEHLTENNRL 650
MCVTCTKQQP GYKDGCKKAV YRDALKQMLI SDPPVVLTLH LKRFQQVAYS 700
VCKVNRHVQF PQILDLAPFC SLNCTGVKEG ETQVLYSLYG IVEHSGTMRS 750
GHYTAYVKSR PSTHNCVQNG TAAASGDAEA SKGSWFHISD SSVHPVPEAK 800
VQSSQAYLLF YEKIS 815
Length:815
Mass (Da):90,450
Last modified:November 13, 2007 - v1
Checksum:i50CF71DC500EE191
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CR854897 Genomic DNA. Translation: CAP09451.1.
RefSeqiNP_001139569.1. NM_001146097.1.
UniGeneiDr.24329.
Dr.99665.

Genome annotation databases

EnsembliENSDART00000085645; ENSDARP00000080080; ENSDARG00000060633.
GeneIDi569700.
KEGGidre:569700.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CR854897 Genomic DNA. Translation: CAP09451.1 .
RefSeqi NP_001139569.1. NM_001146097.1.
UniGenei Dr.24329.
Dr.99665.

3D structure databases

ProteinModelPortali A8HAL1.
SMRi A8HAL1. Positions 22-142.
ModBasei Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSDART00000085645 ; ENSDARP00000080080 ; ENSDARG00000060633 .
GeneIDi 569700.
KEGGi dre:569700.

Organism-specific databases

CTDi 10600.

Phylogenomic databases

eggNOGi COG5560.
GeneTreei ENSGT00750000117419.
HOGENOMi HOG000154755.
HOVERGENi HBG062704.
KOi K11844.
OMAi ECSIQHC.
OrthoDBi EOG7J9VNZ.
PhylomeDBi A8HAL1.
TreeFami TF326075.

Miscellaneous databases

NextBioi 20889807.
PROi A8HAL1.

Gene expression databases

Bgeei A8HAL1.

Family and domain databases

Gene3Di 3.30.40.10. 1 hit.
HAMAPi MF_03062. UBP16.
InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view ]
Pfami PF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
[Graphical view ]
PROSITEi 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. "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(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Tuebingen.

Entry informationi

Entry nameiUBP16_DANRE
AccessioniPrimary (citable) accession number: A8HAL1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: November 13, 2007
Last modified: September 3, 2014
This is version 58 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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