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Q2KJ09 (UBP16_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 67. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:Usp16
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length826 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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. In resting B- and T-lymphocytes, phosphorylation by AURKB leads to enhance its activity, thereby maintaining transcription in resting lymphocytes. Regulates Hox gene expression via histone H2A deubiquitination. Prefers nucleosomal substrates. Does not deubiquitinate histone H2B By similarity. HAMAP-Rule MF_03062

Catalytic activity

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). HAMAP-Rule MF_03062

Subunit structure

Homotetramer By similarity. HAMAP-Rule MF_03062

Subcellular location

Nucleus By similarity HAMAP-Rule MF_03062.

Domain

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. HAMAP-Rule MF_03062

Post-translational modification

Phosphorylated at the onset of mitosis and dephosphorylated during the metaphase/anaphase transition. Phosphorylation by AURKB enhances the deubiquitinase activity By similarity. HAMAP-Rule MF_03062

Sequence similarities

Belongs to the peptidase C19 family. USP16 subfamily.

Contains 1 UBP-type zinc finger.

Contains 1 USP domain.

Sequence caution

The sequence AAI12387.1 differs from that shown. Reason: Contaminating sequence. Potential poly-A sequence.

Ontologies

Keywords
   Biological processCell cycle
Cell division
Mitosis
Transcription
Transcription regulation
Ubl conjugation pathway
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   DomainZinc-finger
   LigandMetal-binding
Zinc
   Molecular functionActivator
Chromatin regulator
Hydrolase
Protease
Thiol protease
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcellular response to DNA damage stimulus

Inferred from sequence or structural similarity. Source: UniProtKB

histone H2A K63-linked deubiquitination

Inferred from sequence or structural similarity. Source: UniProtKB

histone deubiquitination

Inferred from sequence or structural similarity. Source: UniProtKB

mitosis

Inferred from sequence or structural similarity. Source: UniProtKB

monoubiquitinated histone H2A deubiquitination

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of transcription from RNA polymerase II promoter

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of transcription, DNA-templated

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of translational elongation

Inferred from sequence or structural similarity. Source: UniProtKB

protein homotetramerization

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of transcription from RNA polymerase II promoter

Inferred from sequence or structural similarity. Source: UniProtKB

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

ubiquitin-dependent protein catabolic process

Inferred from electronic annotation. Source: InterPro

   Cellular_componentnucleus

Inferred from sequence or structural similarity. Source: UniProtKB

   Molecular_functioncysteine-type endopeptidase activity

Inferred from sequence or structural similarity. Source: UniProtKB

histone binding

Inferred from sequence or structural similarity. Source: UniProtKB

transcription coactivator activity

Inferred from sequence or structural similarity. Source: UniProtKB

ubiquitin binding

Inferred from sequence or structural similarity. Source: UniProtKB

ubiquitin thiolesterase activity

Inferred from sequence or structural similarity. Source: UniProtKB

ubiquitin-specific protease activity

Inferred from sequence or structural similarity. Source: UniProtKB

zinc ion binding

Inferred from sequence or structural similarity. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q2KJ09-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q2KJ09-2)

The sequence of this isoform differs from the canonical sequence as follows:
     149-149: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 826826Ubiquitin carboxyl-terminal hydrolase 16 HAMAP-Rule MF_03062
PRO_0000367504

Regions

Domain195 – 825631USP
Zinc finger46 – 12479UBP-type HAMAP-Rule MF_03062

Sites

Active site2041Nucleophile By similarity
Active site7601Proton acceptor By similarity
Metal binding241Zinc 1 By similarity
Metal binding261Zinc 1 By similarity
Metal binding481Zinc 2 By similarity
Metal binding511Zinc 2 By similarity
Metal binding731Zinc 3 By similarity
Metal binding761Zinc 3 By similarity
Metal binding811Zinc 2 By similarity
Metal binding891Zinc 2 By similarity
Metal binding931Zinc 3 By similarity
Metal binding1021Zinc 3 By similarity
Metal binding1151Zinc 1 By similarity
Metal binding1181Zinc 1 By similarity

Amino acid modifications

Modified residue4141Phosphoserine By similarity

Natural variations

Alternative sequence1491Missing in isoform 2.
VSP_036725

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified March 24, 2009. Version 2.
Checksum: 2DCC40B25676BA5E

FASTA82693,762
        10         20         30         40         50         60 
MGKKRTKGKS VPEKASSEST EPMCRHLRKG LEQGNLKKAL VNVEWNICQD CKTDNKVKDK 

        70         80         90        100        110        120 
SEEEAEDPSV WLCLKCGHQG CGRDSQEQHA LKHYTTPRSE PHYLVLSLDN WSVWCYKCDE 

       130        140        150        160        170        180 
EIKYCSSNRL GQVVDYVRKQ AGRITSKPAE KNNGHIELEN KKLEKESKNE QEREKSESMA 

       190        200        210        220        230        240 
KENIPLDSAS QITVKGLSNL GNTCFFNAVM QNLSQTPVLR ELLKEVKMSG TIVKIEPPDL 

       250        260        270        280        290        300 
ALTEPLEVNL EPPGPLTLAM SQFLNEMQEN KKRIVTPKEL FSQVCKKATR FKGYQQQDSQ 

       310        320        330        340        350        360 
ELLRYLLDGM RAEEHQRVSK GILKAFGNST EKLDEEVKNK VKDYEKKKAI PSFVDRIFGG 

       370        380        390        400        410        420 
ELTSTIMCDD CRTVSLVHES FLDLSLPVLD DQSGKKNIND KNVKKTMEEE DKDSEEEKDD 

       430        440        450        460        470        480 
SYMKTRSDVP SGTSKHTQKK AKKQAKKQAK NQRRQQKIQE RFLHFNEICT TNYTEDNDHE 

       490        500        510        520        530        540 
AETALPGEGE VDTEFNRGSQ EELTQTELCA NQKDVNGQEE MIESAADERK CPEHPEVKSV 

       550        560        570        580        590        600 
STESDLGSLT SAPECPRDLN GAFLEERTSG ELDITNGLKN LTLNAAVDPD EISIEILNDS 

       610        620        630        640        650        660 
HSPALKVYEV MNEDPETAFC TLANREAFST DECSIQHCLY QFTRNEKLQD ANKLLCEVCT 

       670        680        690        700        710        720 
RRQCNGPKAN IKGERKHVYT NAKKQMLVSL APPVLTLHLK RFQQAGFNLR KVNKHIKFPE 

       730        740        750        760        770        780 
ILDLAPFCTL KCKNVAEEST RVLYSLYGVV EHSGTMRSGH YTAYAKERTA SCHLSNLVLH 

       790        800        810        820 
GDIPQDCEME STKGQWFHIS DTHVQAVPIT KVLNSQAYLL FYERIL 

« Hide

Isoform 2 [UniParc].

Checksum: 9F57C2952CF266B6
Show »

FASTA82593,691

References

[1]Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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] OF 1-659 (ISOFORM 2).
Tissue: Prostate.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CH473989 Genomic DNA. Translation: EDM10641.1.
BC112386 mRNA. Translation: AAI12387.1. Sequence problems.
RefSeqNP_001093971.1. NM_001100501.1.
XP_006248077.1. XM_006248015.1.
UniGeneRn.55800.

3D structure databases

ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING10116.ENSRNOP00000002173.

Protein family/group databases

MEROPSC19.050.

Proteomic databases

PaxDbQ2KJ09.
PRIDEQ2KJ09.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000002173; ENSRNOP00000002173; ENSRNOG00000001598. [Q2KJ09-1]
GeneID288306.
KEGGrno:288306.
UCSCRGD:1307192. rat. [Q2KJ09-1]

Organism-specific databases

CTD10600.
RGD1307192. Usp16.

Phylogenomic databases

eggNOGCOG5207.
GeneTreeENSGT00750000117419.
HOGENOMHOG000154755.
HOVERGENHBG062704.
InParanoidQ2KJ09.
KOK11844.
OMACKNVAEE.
OrthoDBEOG7J9VNZ.
PhylomeDBQ2KJ09.
TreeFamTF326075.

Gene expression databases

GenevestigatorQ2KJ09.

Family and domain databases

Gene3D3.30.40.10. 1 hit.
HAMAPMF_03062. UBP16.
InterProIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view]
PfamPF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
[Graphical view]
PROSITEPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
PS50271. ZF_UBP. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio627930.
PROQ2KJ09.

Entry information

Entry nameUBP16_RAT
AccessionPrimary (citable) accession number: Q2KJ09
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: March 24, 2009
Last modified: April 16, 2014
This is version 67 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries