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Q2KJ09

- UBP16_RAT

UniProt

Q2KJ09 - UBP16_RAT

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Protein

Ubiquitin carboxyl-terminal hydrolase 16

Gene

Usp16

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli

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. 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.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 1UniRule annotation
Metal bindingi26 – 261Zinc 1UniRule annotation
Metal bindingi48 – 481Zinc 2UniRule annotation
Metal bindingi51 – 511Zinc 2UniRule annotation
Metal bindingi73 – 731Zinc 3UniRule annotation
Metal bindingi76 – 761Zinc 3UniRule annotation
Metal bindingi81 – 811Zinc 2UniRule annotation
Metal bindingi89 – 891Zinc 2UniRule annotation
Metal bindingi93 – 931Zinc 3UniRule annotation
Metal bindingi102 – 1021Zinc 3UniRule annotation
Metal bindingi115 – 1151Zinc 1UniRule annotation
Metal bindingi118 – 1181Zinc 1UniRule annotation
Active sitei204 – 2041NucleophileUniRule annotation
Active sitei760 – 7601Proton acceptorUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri46 – 12479UBP-typeUniRule annotationAdd
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-specific protease activity Source: UniProtKB
  6. ubiquitin thiolesterase activity Source: UniProtKB
  7. zinc ion binding Source: UniProtKB

GO - Biological processi

  1. cellular response to DNA damage stimulus Source: UniProtKB
  2. histone deubiquitination Source: UniProtKB
  3. histone H2A K63-linked deubiquitination Source: UniProtKB
  4. mitotic nuclear division Source: UniProtKB
  5. monoubiquitinated histone H2A deubiquitination Source: UniProtKB
  6. positive regulation of transcription, DNA-templated Source: UniProtKB
  7. positive regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  8. positive regulation of translational elongation Source: UniProtKB
  9. protein homotetramerization Source: UniProtKB
  10. regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  11. transcription, DNA-templated Source: UniProtKB-KW
  12. 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

Protein family/group databases

MEROPSiC19.050.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase 16UniRule annotation (EC:3.4.19.12UniRule annotation)
Alternative name(s):
Deubiquitinating enzyme 16UniRule annotation
Ubiquitin thioesterase 16UniRule annotation
Ubiquitin-specific-processing protease 16UniRule annotation
Gene namesi
Name:Usp16
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494: Chromosome 11

Organism-specific databases

RGDi1307192. Usp16.

Subcellular locationi

Nucleus 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 – 826826Ubiquitin carboxyl-terminal hydrolase 16PRO_0000367504Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei414 – 4141PhosphoserineBy similarity

Post-translational modificationi

Phosphorylated at the onset of mitosis and dephosphorylated during the metaphase/anaphase transition. Phosphorylation by AURKB enhances the deubiquitinase activity.UniRule annotation

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ2KJ09.
PRIDEiQ2KJ09.

Expressioni

Gene expression databases

GenevestigatoriQ2KJ09.

Interactioni

Subunit structurei

Homotetramer.UniRule annotation

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000002173.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini195 – 825631USPAdd
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.UniRule annotation

Sequence similaritiesi

Belongs to the peptidase C19 family. USP16 subfamily.UniRule annotation
Contains 1 UBP-type zinc finger.UniRule annotation
Contains 1 USP domain.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri46 – 12479UBP-typeUniRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG5207.
GeneTreeiENSGT00670000097750.
HOGENOMiHOG000154755.
HOVERGENiHBG062704.
InParanoidiQ2KJ09.
KOiK11844.
OMAiECSIQHC.
OrthoDBiEOG7J9VNZ.
PhylomeDBiQ2KJ09.
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]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q2KJ09-1) [UniParc]FASTAAdd to Basket

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.

« Hide

        10         20         30         40         50
MGKKRTKGKS VPEKASSEST EPMCRHLRKG LEQGNLKKAL VNVEWNICQD
60 70 80 90 100
CKTDNKVKDK SEEEAEDPSV WLCLKCGHQG CGRDSQEQHA LKHYTTPRSE
110 120 130 140 150
PHYLVLSLDN WSVWCYKCDE EIKYCSSNRL GQVVDYVRKQ AGRITSKPAE
160 170 180 190 200
KNNGHIELEN KKLEKESKNE QEREKSESMA KENIPLDSAS QITVKGLSNL
210 220 230 240 250
GNTCFFNAVM QNLSQTPVLR ELLKEVKMSG TIVKIEPPDL ALTEPLEVNL
260 270 280 290 300
EPPGPLTLAM SQFLNEMQEN KKRIVTPKEL FSQVCKKATR FKGYQQQDSQ
310 320 330 340 350
ELLRYLLDGM RAEEHQRVSK GILKAFGNST EKLDEEVKNK VKDYEKKKAI
360 370 380 390 400
PSFVDRIFGG ELTSTIMCDD CRTVSLVHES FLDLSLPVLD DQSGKKNIND
410 420 430 440 450
KNVKKTMEEE DKDSEEEKDD SYMKTRSDVP SGTSKHTQKK AKKQAKKQAK
460 470 480 490 500
NQRRQQKIQE RFLHFNEICT TNYTEDNDHE AETALPGEGE VDTEFNRGSQ
510 520 530 540 550
EELTQTELCA NQKDVNGQEE MIESAADERK CPEHPEVKSV STESDLGSLT
560 570 580 590 600
SAPECPRDLN GAFLEERTSG ELDITNGLKN LTLNAAVDPD EISIEILNDS
610 620 630 640 650
HSPALKVYEV MNEDPETAFC TLANREAFST DECSIQHCLY QFTRNEKLQD
660 670 680 690 700
ANKLLCEVCT RRQCNGPKAN IKGERKHVYT NAKKQMLVSL APPVLTLHLK
710 720 730 740 750
RFQQAGFNLR KVNKHIKFPE ILDLAPFCTL KCKNVAEEST RVLYSLYGVV
760 770 780 790 800
EHSGTMRSGH YTAYAKERTA SCHLSNLVLH GDIPQDCEME STKGQWFHIS
810 820
DTHVQAVPIT KVLNSQAYLL FYERIL
Length:826
Mass (Da):93,762
Last modified:March 24, 2009 - v2
Checksum:i2DCC40B25676BA5E
GO
Isoform 2 (identifier: Q2KJ09-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     149-149: Missing.

Note: No experimental confirmation available.

Show »
Length:825
Mass (Da):93,691
Checksum:i9F57C2952CF266B6
GO

Sequence cautioni

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

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei149 – 1491Missing in isoform 2. 1 PublicationVSP_036725

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CH473989 Genomic DNA. Translation: EDM10641.1.
BC112386 mRNA. Translation: AAI12387.1. Sequence problems.
RefSeqiNP_001093971.1. NM_001100501.1. [Q2KJ09-2]
XP_006248077.1. XM_006248015.2. [Q2KJ09-1]
UniGeneiRn.55800.

Genome annotation databases

EnsembliENSRNOT00000002173; ENSRNOP00000002173; ENSRNOG00000001598. [Q2KJ09-1]
GeneIDi288306.
KEGGirno:288306.
UCSCiRGD:1307192. rat. [Q2KJ09-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CH473989 Genomic DNA. Translation: EDM10641.1 .
BC112386 mRNA. Translation: AAI12387.1 . Sequence problems.
RefSeqi NP_001093971.1. NM_001100501.1. [Q2KJ09-2 ]
XP_006248077.1. XM_006248015.2. [Q2KJ09-1 ]
UniGenei Rn.55800.

3D structure databases

ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 10116.ENSRNOP00000002173.

Protein family/group databases

MEROPSi C19.050.

Proteomic databases

PaxDbi Q2KJ09.
PRIDEi Q2KJ09.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSRNOT00000002173 ; ENSRNOP00000002173 ; ENSRNOG00000001598 . [Q2KJ09-1 ]
GeneIDi 288306.
KEGGi rno:288306.
UCSCi RGD:1307192. rat. [Q2KJ09-1 ]

Organism-specific databases

CTDi 10600.
RGDi 1307192. Usp16.

Phylogenomic databases

eggNOGi COG5207.
GeneTreei ENSGT00670000097750.
HOGENOMi HOG000154755.
HOVERGENi HBG062704.
InParanoidi Q2KJ09.
KOi K11844.
OMAi ECSIQHC.
OrthoDBi EOG7J9VNZ.
PhylomeDBi Q2KJ09.
TreeFami TF326075.

Miscellaneous databases

NextBioi 627930.
PROi Q2KJ09.

Gene expression databases

Genevestigatori Q2KJ09.

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. 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.

Entry informationi

Entry nameiUBP16_RAT
AccessioniPrimary (citable) accession number: Q2KJ09
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: March 24, 2009
Last modified: November 26, 2014
This is version 72 of the entry and version 2 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