iUUCD 2.0 - integrated annotations for ubiquitin and ubiquitin-like conjugation database

Protein
Gene
Annotation
Details
Classification
Domain Profile
Function
Protein Sequence
Nucleotide Sequence
Keyword
GO
Orthology
TOP

Basic Information

Integrated Annotations

Tag

Content

iUUCD ID

IUUC-Hsa-046546

UUCD1 version

UUC-HoS-01136

Ensembl Protein ID

ENSP00000263966.3

UniProt Accession

Q92995; A8K2S3; B4DYF3; D3DNS2; Q96B25; UBP13_HUMAN

Genbank Protein ID

AAC63405.1; BAF83027.1; BAG63715.1; EAW78383.1; EAW78384.1; AAH16146.1

Protein Name

Ubiquitin carboxyl-terminal hydrolase 13; Deubiquitinating enzyme 13; Isopeptidase T-3; Ubiquitin thioesterase 13; Ubiquitin-specific-processing protease 13

Genbank Nucleotide ID

U75362; AK290338; AK302404; AC007687; CH471052; BC016146

Gene Name

USP13; ISOT3

Ensembl Information

Ensembl Gene ID	Ensembl Transcript ID	Ensembl Protein ID
ENSG00000058056.8	ENST00000263966.7	ENSP00000263966.3
ENSG00000058056.8	ENST00000497380.1	ENSP00000418651.1
ENSG00000058056.8	ENST00000497155.1	ENSP00000420057.1

Annotation

Cancer Mutation
TCGA	ICGC	COSMIC	CGAP
IntOGen
Single Nucleotide Polymorphisms (SNP)
dbSNP
mRNA Expression
GEO	ArrayExpress	TCGA	ICGC
COSMIC	THPA	HPM
DNA & RNA Element
UTRdb	AREsite	circBase	circRNADb
CircNet	miRTarBase	microRNA	TRANSFAC
TargetScan	RepTar	miRNAMap	SomamiR
miRcode	RAID2
Protein-protein Interaction
IID	iRefIndex	PINA	HINT
Mentha	InWeb_IM
Protein 3D Structure
PDB
Disease-associated Information
GWASdb	OMIM
Post-translational Modifications (PTMs)
CPLM	dbPAF	PhosphositePlus	dbPTM
HPRD	Phospho.ELM	UniProt	BioGRID
mUbiSiDa
DNA Methylation
TCGA	ICGC	COSMIC
Protein Expression/Proteomics
THPA	HPM	GPMDB

Status

Reviewed

Details

Family	Domain	References (PMIDs)
DUB/USP	USP	12401499
UBD/Alpha-Helix/UBA	UBA	22216260

Classification

Family	E-value	Score	Start	End
DUB/USP	3.50e-57	195.8	336	860
UBD/Alpha-Helix/UBA	4.60e-20	72.7	730	767

Active Site

Position(s)	Description	Evidence
345	Nucleophile	ECO:0000305}
823	Proton acceptor	ECO:0000255\|PROSITE-ProRule:PRU10092, ECO:0000255\|PROSITE-ProRule:PRU10093}

Domain Profile

DUB/USP

   S: 1    tGlkNlgNtCYmNSvLQcLsnipelrelllekkkeklneenpkepkgellkslqklfeel......................wkskkkavsp 70
           tGlkNlgN+CY+ Sv+Q++++ipe+++++  + ++ ++ + p +p++++ ++++kl + l                       k +++ +sp
   Q: 336  TGLKNLGNSCYLSSVMQAIFSIPEFQRAYVGNLPRIFDYS-PLDPTQDFNTQMTKLGHGLlsgqyskppvkselieqvmkeeHKPQQNGISP 426
           7******************************788777765.79*****************8888888888888877765543388888**** PP
   S: 71   rellkalkkeaeefsgyeqqDaqEflaflldqleeelkkeknkpkeeeeeedkselsdeaeekkkkknkslisdlFqgqlksqikclecdnv 162
           r++++ ++k ++efs+++qqDaqEf+ +l++ +e++                               +++  sd+F++ ++++i+c + ++v
   Q: 427  RMFKAFVSKSHPEFSSNRQQDAQEFFLHLVNLVERNR-----------------------------IGSENPSDVFRFLVEERIQCCQTRKV 489
           **********************************998.............................688899******************** PP
   S: 163  ssreepfldlslpvpgkeetkke...........................slqdcLesftkeeelegenkyycekckkkqeaekklklkklP 227
             +e   + ++lpv ++  t+k                             ++ cL++f+++e++++   ++++  ++k+  +k+ ++ ++P
   Q: 490  RYTERVDYLMQLPVAMEAATNKDeliayeltrreaeanrrplpelvrakiPFSACLQAFSEPENVDD---FWSSALQAKSAGVKTSRFASFP 578
           9999999999999999998887799****************************************97...********************** PP
   S: 228  evLilhLkRfsfseeqksrekinkkvefpleLdlspfcts.................................................... 267
           e+L++++k+f+f  + ++++k++ ++++p+ Ld+++  ++                                                    
   Q: 579  EYLVVQIKKFTFGLD-WVPKKFDVSIDMPDLLDINHLRARglqpgeeelpdisppivipddskdrlmnqlidpsdidessvmqlaemgfple 669
           ************997.*******************999889999999999999999998888888888888888888888877777777777 PP
   S: 268  ........................................................................................peek 271
                                                                                                   +   
   Q: 670  acrkavyftgnmgaevafnwiivhmeepdfaepltmpgyggaasagasvfgasgldnqppeeivaiitsmgfqrnqaiqalratnnnlE--- 758
           77777777777777777777777777777777777777777777777777777777666666666666666666666666665555550... PP
   S: 272  qke...........................................kkkYeLiavvvHsG.slssGHYvayvknekgkWllfdDskVtevke 319
             +                                           + +YeL+a ++H+G s+ sGHY++++k+ +g+W+ ++D+kV ++  
   Q: 759  --RaldwifshpefeedsdfviemennananiiseakpegprvkdgSGTYELFAFISHMGtSTMSGHYICHIKK-EGRWVIYNDHKVCAS-- 845
           ..05555555555555555666666666677788888888888888****************************.9***********999.. PP
   S: 320  eevleetgstaYvlfYkr 337
           e+  +   + +Y++fY+r
   Q: 846  ERPPK---DLGYMYFYRR 860
           78888...99******98 PP

UBD/Alpha-Helix/UBA

   S: 4    edkleqlveMGFdreealqaLraannnleaAveyLldg 41
           e++++ +++MGF r++a+qaLra+nnnle+A+++++++
   Q: 730  EEIVAIITSMGFQRNQAIQALRATNNNLERALDWIFSH 767
           899*********************************97 PP

Organism

Homo sapiens

Functional Description
(View)

Deubiquitinase that mediates deubiquitination of target proteins such as BECN1, MITF, SKP2 and USP10 and is involved in various processes such as autophagy and endoplasmic reticulum-associated degradation (ERAD). Component of a regulatory loop that controls autophagy and p53/TP53 levels: mediates deubiquitination of BECN1, a key regulator of autophagy, leading to stabilize the PIK3C3/VPS34-containing complexes. Also deubiquitinates USP10, an essential regulator of p53/TP53 stability. In turn, PIK3C3/VPS34-containing complexes regulate USP13 stability, suggesting the existence of a regulatory system by which PIK3C3/VPS34-containing complexes regulate p53/TP53 protein levels via USP10 and USP13. Recruited by nuclear UFD1 and mediates deubiquitination of SKP2, thereby regulating endoplasmic reticulum-associated degradation (ERAD). Also regulates ERAD through the deubiquitination of UBL4A a component of the BAG6/BAT3 complex. Mediates stabilization of SIAH2 independently of deubiquitinase activity: binds ubiquitinated SIAH2 and acts by impairing SIAH2 autoubiquitination. Has a weak deubiquitinase activity in vitro and preferentially cleaves 'Lys-63'-linked polyubiquitin chains. In contrast to USP5, it is not able to mediate unanchored polyubiquitin disassembly. Able to cleave ISG15 in vitro; however, additional experiments are required to confirm such data.

Protein Sequence
(Fasta)

MQRRGALFGM PGGSGGRKMA AGDIGELLVP HMPTIRVPRS GDRVYKNECA FSYDSPNSEG 60
GLYVCMNTFL AFGREHVERH FRKTGQSVYM HLKRHVREKV RGASGGALPK RRNSKIFLDL 120

It may take some time, please wait.

Nucleotide Sequence
(Fasta)

GGCCTCCTCG GAGTTGCCCC TCTGCAAGCC AACAATTCGG GATAGAAAAC ACCTCCGTGG 60
TGTTTTCCCG GGGCCCTCCC GCGCCGCGTT CGGCCGCCAG CCCGCTCGAG CTCCCGCGCC 120

It may take some time, please wait.

Sequence Source

Ensembl

Keyword

KW-0002--3D-structure
KW-0025--Alternative splicing
KW-0072--Autophagy
KW-0181--Complete proteome
KW-0378--Hydrolase
KW-0479--Metal-binding
KW-0597--Phosphoprotein
KW-0645--Protease
KW-1185--Reference proteome
KW-0677--Repeat
KW-0788--Thiol protease
KW-0833--Ubl conjugation pathway
KW-0862--Zinc
KW-0863--Zinc-finger

Interpro

IPR001394--Peptidase_C19_UCH
IPR015940--UBA
IPR009060--UBA-like
IPR016652--Ubiquitinyl_hydrolase
IPR018200--USP_CS
IPR028889--USP_dom
IPR013083--Znf_RING/FYVE/PHD
IPR001607--Znf_UBP

PROSITE

PS50030--UBA
PS00972--USP_1
PS00973--USP_2
PS50235--USP_3
PS50271--ZF_UBP

Pfam

PF00627--UBA
PF00443--UCH
PF02148--zf-UBP

SMART

SM00165--UBA
SM00290--ZnF_UBP

Gene Ontology

GO:0005829--C:cytosol
GO:0005654--C:nucleoplasm
GO:1904288--F:BAT3 complex binding
GO:0051087--F:chaperone binding
GO:0004197--F:cysteine-type endopeptidase activity
GO:0070628--F:proteasome binding
GO:0004843--F:thiol-dependent ubiquitin-specific protease activity
GO:0036459--F:thiol-dependent ubiquitinyl hydrolase activity
GO:0043130--F:ubiquitin binding
GO:0031625--F:ubiquitin protein ligase binding
GO:0044389--F:ubiquitin-like protein ligase binding
GO:1904454--F:ubiquitin-specific protease activity involved in positive regulation of ERAD pathway
GO:0008270--F:zinc ion binding
GO:0006914--P:autophagy
GO:0008283--P:cell proliferation
GO:1904378--P:maintenance of unfolded protein involved in ERAD pathway
GO:0030318--P:melanocyte differentiation
GO:1904294--P:positive regulation of ERAD pathway
GO:0016579--P:protein deubiquitination
GO:0035523--P:protein K29-linked deubiquitination
GO:0044313--P:protein K6-linked deubiquitination
GO:0070536--P:protein K63-linked deubiquitination
GO:0050821--P:protein stabilization
GO:0010506--P:regulation of autophagy
GO:0006355--P:regulation of transcription, DNA-templated
GO:0006511--P:ubiquitin-dependent protein catabolic process

KEGG

hsa:8975

Orthology

iUUCD ID	Species	Identity	E-value	Score
IUUC-Aml-001356	Ailuropoda melanoleuca	98.25	0.00e+00	1612.00
IUUC-Apl-003712	Anas platyrhynchos	83.72	0.00e+00	1354.00
IUUC-Aca-004634	Anolis carolinensis	83.43	0.00e+00	1403.00
IUUC-Ame-011470	Astyanax mexicanus	74.45	0.00e+00	1288.00
IUUC-Bta-013349	Bos taurus	98.03	0.00e+00	1653.00
IUUC-Cja-019021	Callithrix jacchus	97.45	0.00e+00	1598.00
IUUC-Cfa-020614	Canis familiaris	98.49	0.00e+00	1624.00
IUUC-Cpo-022484	Cavia porcellus	98.03	0.00e+00	1512.00
IUUC-Csa-024078	Chlorocebus sabaeus	99.54	0.00e+00	1636.00
IUUC-Cho-024522	Choloepus hoffmanni	81.41	0.00e+00	1181.00
IUUC-Cme-027335	Cyanidioschyzon merolae	25.58	3.00e-53	204.00
IUUC-Dre-027651	Danio rerio	74.94	0.00e+00	1349.00
IUUC-Dno-028975	Dasypus novemcinctus	98.27	0.00e+00	1621.00
IUUC-Dor-030130	Dipodomys ordii	73.90	0.00e+00	1075.00
IUUC-Ete-032251	Echinops telfairi	82.78	0.00e+00	1282.00
IUUC-Eca-033568	Equus caballus	98.88	0.00e+00	1514.00
IUUC-Eeu-034612	Erinaceus europaeus	79.80	0.00e+00	1151.00
IUUC-Fca-036280	Felis catus	98.76	0.00e+00	1510.00
IUUC-Fal-036610	Ficedula albicollis	84.52	0.00e+00	1330.00
IUUC-Gmo-038906	Gadus morhua	72.66	0.00e+00	1254.00
IUUC-Gga-041215	Gallus gallus	83.24	0.00e+00	1429.00
IUUC-Gac-042441	Gasterosteus aculeatus	72.25	0.00e+00	1267.00
IUUC-Ggo-044446	Gorilla gorilla	99.54	0.00e+00	1635.00
IUUC-Itr-048147	Ictidomys tridecemlineatus	89.67	0.00e+00	1435.00
IUUC-Lch-050425	Latimeria chalumnae	77.85	0.00e+00	1354.00
IUUC-Loc-052072	Lepisosteus oculatus	77.60	0.00e+00	1308.00
IUUC-Laf-053909	Loxodonta africana	96.42	0.00e+00	1608.00
IUUC-Mcc-054686	Macaca mulatta	99.54	0.00e+00	1637.00
IUUC-Meu-056361	Macropus eugenii	80.45	0.00e+00	1306.00
IUUC-Mga-059972	Meleagris gallopavo	79.11	0.00e+00	1296.00
IUUC-Mmr-060916	Microcebus murinus	97.80	0.00e+00	1615.00
IUUC-Mdo-062302	Monodelphis domestica	89.40	0.00e+00	1511.00
IUUC-Mmu-063639	Mus musculus	95.48	0.00e+00	1604.00
IUUC-Mpu-066533	Mustela putorius furo	98.61	0.00e+00	1625.00
IUUC-Mlu-067786	Myotis lucifugus	91.67	0.00e+00	1470.00
IUUC-Nle-069997	Nomascus leucogenys	99.62	0.00e+00	1504.00
IUUC-Ont-071859	Oreochromis niloticus	72.58	0.00e+00	1271.00
IUUC-Oan-072959	Ornithorhynchus anatinus	88.70	6.00e-128	449.00
IUUC-Ocu-074265	Oryctolagus cuniculus	98.02	0.00e+00	1602.00
IUUC-Ola-087344	Oryzias latipes	71.61	0.00e+00	1280.00
IUUC-Oga-088734	Otolemur garnettii	98.32	0.00e+00	1556.00
IUUC-Oar-089636	Ovis aries	98.02	0.00e+00	1573.00
IUUC-Ptr-090982	Pan troglodytes	99.77	0.00e+00	1638.00
IUUC-Pan-091991	Papio anubis	99.65	0.00e+00	1638.00
IUUC-Psi-093509	Pelodiscus sinensis	86.37	0.00e+00	1459.00
IUUC-Pfo-096029	Poecilia formosa	74.16	0.00e+00	1318.00
IUUC-Pab-098672	Pongo abelii	95.48	0.00e+00	1537.00
IUUC-Pca-100860	Procavia capensis	74.07	0.00e+00	1041.00
IUUC-Pva-102545	Pteropus vampyrus	90.15	0.00e+00	1476.00
IUUC-Rno-105210	Rattus norvegicus	94.90	0.00e+00	1588.00
IUUC-Sar-113733	Sorex araneus	96.29	0.00e+00	771.00
IUUC-Tgu-116591	Taeniopygia guttata	84.49	0.00e+00	1429.00
IUUC-Tru-118627	Takifugu rubripes	70.83	0.00e+00	1280.00
IUUC-Tsy-119278	Tarsius syrichta	89.96	0.00e+00	1355.00
IUUC-Tni-120804	Tetraodon nigroviridis	73.90	0.00e+00	1309.00
IUUC-Tbe-127699	Tupaia belangeri	79.19	0.00e+00	872.00
IUUC-Ttr-128295	Tursiops truncatus	89.93	0.00e+00	1472.00
IUUC-Vpa-130170	Vicugna pacos	87.11	0.00e+00	1333.00
IUUC-Xtr-132809	Xenopus tropicalis	74.01	0.00e+00	1272.00

Created Date

25-Jun-2017

Functional Description

Protein Fasta Sequence

Nucleotide Fasta Sequence