LLPS-Hos-2138
USP13

▼ OVERVIEW

Status: Reviewed
Protein Name: Ubiquitin carboxyl-terminal hydrolase 13; Deubiquitinating enzyme 13; Isopeptidase T-3; ISOT-3; Ubiquitin thioesterase 13; Ubiquitin-specific-processing protease 13
Gene Name: USP13, ISOT3
Ensembl Gene: ENSG00000058056.8
Ensembl Protein: ENSP00000263966.3
Organism: Homo sapiens
Taxa ID: 9606
LLPS Type: Others
PDB: 2L80 (A) More


▼ PROPERTY


——— Disorder propensity (calculated by IUPred2A)

▼ Classification

Condensates:
CondensateDescriptionTissue/CellPMIDs
Nucleolus
"...Thus, we analyzed the orthologous groups of the remaining 2316 identified proteins to the human nucleolar proteins. We detected 361 orthologues in NoPDB from the 2316 A. thaliana proteins."
N/A26980300

▼ FUNCTION

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.

▼ SEQUENCE

Protein Sequence (FASTA)
1     MQRRGALFGM  PGGSGGRKMA  AGDIGELLVP  HMPTIRVPRS  GDRVYKNECA  FSYDSPNSEG  60
61    GLYVCMNTFL  AFGREHVERH  FRKTGQSVYM  HLKRHVREKV  RGASGGALPK  RRNSKIFLDL  120
121   DTDDDLNSDD  YEYEDEAKLV  IFPDHYEIAL  PNIEELPALV  TIACDAVLSS  KSPYRKQDPD  180
181   TWENELPVSK  YANNLTQLDN  GVRIPPSGWK  CARCDLRENL  WLNLTDGSVL  CGKWFFDSSG  240
241   GNGHALEHYR  DMGYPLAVKL  GTITPDGADV  YSFQEEEPVL  DPHLAKHLAH  FGIDMLHMHG  300
301   TENGLQDNDI  KLRVSEWEVI  QESGTKLKPM  YGPGYTGLKN  LGNSCYLSSV  MQAIFSIPEF  360
361   QRAYVGNLPR  IFDYSPLDPT  QDFNTQMTKL  GHGLLSGQYS  KPPVKSELIE  QVMKEEHKPQ  420
421   QNGISPRMFK  AFVSKSHPEF  SSNRQQDAQE  FFLHLVNLVE  RNRIGSENPS  DVFRFLVEER  480
481   IQCCQTRKVR  YTERVDYLMQ  LPVAMEAATN  KDELIAYELT  RREAEANRRP  LPELVRAKIP  540
541   FSACLQAFSE  PENVDDFWSS  ALQAKSAGVK  TSRFASFPEY  LVVQIKKFTF  GLDWVPKKFD  600
601   VSIDMPDLLD  INHLRARGLQ  PGEEELPDIS  PPIVIPDDSK  DRLMNQLIDP  SDIDESSVMQ  660
661   LAEMGFPLEA  CRKAVYFTGN  MGAEVAFNWI  IVHMEEPDFA  EPLTMPGYGG  AASAGASVFG  720
721   ASGLDNQPPE  EIVAIITSMG  FQRNQAIQAL  RATNNNLERA  LDWIFSHPEF  EEDSDFVIEM  780
781   ENNANANIIS  EAKPEGPRVK  DGSGTYELFA  FISHMGTSTM  SGHYICHIKK  EGRWVIYNDH  840
841   KVCASERPPK  DLGYMYFYRR  IPS  863
Nucleotide CDS Sequence (FASTA)
1     ATGCAGCGCC  GGGGCGCCCT  GTTCGGCATG  CCGGGCGGCA  GCGGAGGCAG  GAAGATGGCT  60
61    GCAGGAGACA  TCGGCGAGCT  GCTAGTGCCC  CACATGCCCA  CGATCCGCGT  GCCCAGGTCC  120
121   GGCGACAGGG  TCTACAAGAA  CGAGTGCGCC  TTCTCCTACG  ACTCTCCCAA  TTCTGAAGGT  180
181   GGACTCTATG  TATGCATGAA  TACATTTTTG  GCCTTTGGAA  GGGAACATGT  TGAAAGACAT  240
241   TTTCGAAAAA  CTGGACAGAG  TGTATACATG  CACCTGAAAA  GACATGTGCG  AGAGAAGGTA  300
301   AGAGGGGCGT  CTGGTGGAGC  GTTACCAAAA  AGGAGGAATT  CCAAGATTTT  TTTAGATCTA  360
361   GATACTGATG  ACGATTTAAA  TAGCGACGAT  TATGAATATG  AAGATGAAGC  CAAACTTGTT  420
421   ATATTCCCAG  ATCACTATGA  AATAGCACTA  CCAAATATTG  AGGAGTTACC  AGCCCTGGTA  480
481   ACAATTGCTT  GTGATGCAGT  TCTCAGCTCA  AAATCTCCAT  ACAGAAAGCA  GGACCCAGAC  540
541   ACGTGGGAAA  ATGAATTGCC  AGTATCTAAA  TATGCCAACA  ACCTCACCCA  GCTGGACAAT  600
601   GGAGTCAGGA  TTCCTCCAAG  TGGTTGGAAG  TGTGCCAGAT  GCGACCTGCG  AGAAAACCTC  660
661   TGGTTGAATC  TGACTGACGG  CTCTGTCCTG  TGTGGAAAGT  GGTTCTTTGA  CAGCTCTGGG  720
721   GGCAACGGGC  ATGCGCTGGA  GCATTACAGA  GACATGGGCT  ACCCACTAGC  CGTGAAACTG  780
781   GGAACCATCA  CTCCTGACGG  GGCAGATGTT  TATTCTTTTC  AAGAAGAAGA  ACCTGTTTTG  840
841   GATCCTCATT  TGGCCAAGCA  CTTAGCGCAT  TTTGGAATTG  ATATGCTTCA  TATGCATGGG  900
901   ACAGAGAATG  GGCTCCAGGA  CAATGACATC  AAGCTGAGGG  TCAGTGAGTG  GGAAGTGATC  960
961   CAGGAGTCGG  GCACGAAACT  GAAGCCAATG  TATGGTCCTG  GCTACACGGG  TCTGAAGAAC  1020
1021  CTGGGCAACA  GCTGCTATCT  CAGCTCTGTC  ATGCAGGCCA  TCTTCAGCAT  CCCAGAATTC  1080
1081  CAGAGAGCGT  ATGTAGGAAA  CCTTCCCAGA  ATATTTGACT  ACTCGCCTTT  AGATCCAACA  1140
1141  CAAGATTTCA  ACACACAGAT  GACTAAGTTA  GGACATGGCC  TTCTCTCAGG  CCAGTATTCA  1200
1201  AAGCCTCCGG  TGAAATCTGA  ACTCATTGAA  CAGGTGATGA  AGGAGGAGCA  CAAGCCACAG  1260
1261  CAGAACGGGA  TCTCTCCGCG  CATGTTTAAG  GCCTTTGTAA  GCAAGAGCCA  CCCGGAATTC  1320
1321  TCCTCTAACA  GGCAGCAAGA  TGCCCAGGAA  TTCTTCTTGC  ACCTGGTGAA  TCTAGTAGAG  1380
1381  AGGAACCGCA  TCGGCTCAGA  AAACCCAAGC  GATGTTTTTC  GTTTTTTGGT  GGAAGAACGC  1440
1441  ATTCAGTGCT  GTCAGACCCG  GAAAGTCCGC  TACACGGAGA  GGGTGGATTA  CCTGATGCAG  1500
1501  TTACCTGTGG  CCATGGAGGC  GGCAACCAAC  AAGGATGAAC  TGATCGCTTA  TGAACTAACG  1560
1561  AGAAGGGAAG  CAGAAGCAAA  CAGAAGACCC  CTTCCTGAGT  TGGTACGTGC  CAAGATACCA  1620
1621  TTTAGTGCCT  GCCTTCAGGC  CTTCTCTGAA  CCAGAAAATG  TTGATGATTT  CTGGAGCAGT  1680
1681  GCCCTACAAG  CAAAGTCTGC  GGGTGTGAAA  ACATCTCGCT  TTGCTTCATT  CCCTGAATAC  1740
1741  TTGGTAGTGC  AGATAAAGAA  GTTCACTTTT  GGTCTTGACT  GGGTTCCCAA  AAAATTTGAT  1800
1801  GTTTCTATTG  ATATGCCAGA  CCTACTTGAT  ATCAACCATC  TCCGAGCCAG  GGGGTTACAG  1860
1861  CCAGGAGAGG  AAGAACTTCC  AGACATCAGC  CCCCCCATAG  TCATTCCTGA  TGACTCAAAA  1920
1921  GATCGCCTGA  TGAACCAATT  GATAGACCCA  TCAGACATCG  ATGAGTCATC  AGTGATGCAG  1980
1981  CTGGCCGAGA  TGGGTTTCCC  GCTGGAAGCA  TGTCGCAAGG  CTGTGTACTT  CACTGGAAAT  2040
2041  ATGGGCGCCG  AGGTGGCCTT  CAACTGGATC  ATTGTTCACA  TGGAAGAGCC  AGATTTTGCT  2100
2101  GAGCCGCTGA  CCATGCCTGG  TTATGGAGGG  GCAGCTTCTG  CTGGAGCCTC  TGTTTTTGGT  2160
2161  GCTTCTGGAC  TGGATAACCA  ACCTCCAGAG  GAAATCGTAG  CTATCATCAC  CTCCATGGGA  2220
2221  TTTCAGCGAA  ATCAGGCTAT  TCAGGCACTA  CGAGCAACGA  ATAATAACCT  GGAAAGAGCA  2280
2281  CTGGATTGGA  TCTTTAGCCA  CCCTGAGTTT  GAAGAAGACA  GTGATTTTGT  GATTGAGATG  2340
2341  GAGAATAATG  CCAATGCAAA  CATTATTTCT  GAGGCCAAGC  CCGAAGGACC  TAGAGTCAAG  2400
2401  GATGGATCTG  GAACATATGA  GCTATTTGCA  TTCATCAGTC  ACATGGGAAC  ATCCACAATG  2460
2461  AGTGGTCATT  ACATTTGCCA  TATCAAAAAG  GAAGGAAGAT  GGGTGATTTA  CAATGACCAC  2520
2521  AAAGTTTGTG  CCTCAGAAAG  GCCCCCTAAA  GACCTGGGCT  ACATGTACTT  TTACCGCAGG  2580
2581  ATACCAAGCT  AA  2592

▼ KEYWORD

ID
Family
3D-structure
Alternative splicing
Autophagy
Complete proteome
Hydrolase
Isopeptide bond
Metal-binding
Phosphoprotein
Protease
Reference proteome
Repeat
Thiol protease
Ubl conjugation
Ubl conjugation pathway
Zinc
Zinc-finger

▼ GENE ONTOLOGY

ID
Classification
Description
Cellular Component
Cytosol
Cellular Component
Nucleoplasm
Molecular Function
BAT3 complex binding
Molecular Function
Chaperone binding
Molecular Function
Cysteine-type endopeptidase activity
Molecular Function
Proteasome binding
Molecular Function
Thiol-dependent ubiquitin-specific protease activity
Molecular Function
Thiol-dependent ubiquitinyl hydrolase activity
Molecular Function
Ubiquitin binding
Molecular Function
Ubiquitin protein ligase binding
Molecular Function
Ubiquitin-like protein ligase binding
Molecular Function
Ubiquitin-specific protease activity involved in positive regulation of ERAD pathway
Molecular Function
Zinc ion binding
Biological Process
Autophagy
Biological Process
Cell population proliferation
Biological Process
Maintenance of unfolded protein involved in ERAD pathway
Biological Process
Melanocyte differentiation
Biological Process
Positive regulation of ERAD pathway
Biological Process
Protein deubiquitination
Biological Process
Protein K29-linked deubiquitination
Biological Process
Protein K6-linked deubiquitination
Biological Process
Protein K63-linked deubiquitination
Biological Process
Protein stabilization
Biological Process
Regulation of autophagy
Biological Process
Regulation of transcription, DNA-templated
Biological Process
Ubiquitin-dependent protein catabolic process

▼ KEGG


▼ ORTHOLOGY

DrLLPS IDOrganismIdentityE-valueScore
LLPS-Nol-3780Nomascus leucogenys99.750.01519
LLPS-Paa-3728Papio anubis99.650.01637
LLPS-Mam-4636Macaca mulatta99.540.01636
LLPS-Man-2372Macaca nemestrina99.540.01636
LLPS-Cea-3502Cercocebus atys99.540.01636
LLPS-Chs-0326Chlorocebus sabaeus99.540.01635
LLPS-Maf-3312Macaca fascicularis99.540.01636
LLPS-Pat-0148Pan troglodytes98.840.01621
LLPS-Pap-1803Pan paniscus98.840.01617
LLPS-Gog-1149Gorilla gorilla98.840.01618
LLPS-Eqc-1756Equus caballus98.730.01624
LLPS-Fec-4596Felis catus98.720.01625
LLPS-Mup-3459Mustela putorius furo98.610.01625
LLPS-Caf-1755Canis familiaris98.490.01623
LLPS-Ict-1021Ictidomys tridecemlineatus98.380.01622
LLPS-Sus-0164Sus scrofa98.380.01621
LLPS-Urm-1642Ursus maritimus98.370.01486
LLPS-Otg-0484Otolemur garnettii98.320.01556
LLPS-Aim-3588Ailuropoda melanoleuca98.250.01611
LLPS-Bot-3757Bos taurus98.030.01620
LLPS-Orc-2660Oryctolagus cuniculus98.020.01602
LLPS-Ova-2269Ovis aries98.020.01504
LLPS-Dio-3286Dipodomys ordii97.80.01621
LLPS-Caj-2566Callithrix jacchus97.450.01597
LLPS-Cap-4405Cavia porcellus97.440.01514
LLPS-Loa-3306Loxodonta africana96.420.01594
LLPS-Fud-1396Fukomys damarensis96.280.01474
LLPS-Cas-2717Carlito syrichta95.950.01521
LLPS-Mum-3998Mus musculus95.710.01588
LLPS-Poa-4476Pongo abelii95.480.01538
LLPS-Mea-0914Mesocricetus auratus95.370.01587
LLPS-Ran-3908Rattus norvegicus95.250.01576
LLPS-Myl-4182Myotis lucifugus90.730.01464
LLPS-Mod-4245Monodelphis domestica89.520.01480
LLPS-Sah-3009Sarcophilus harrisii88.810.0 725
LLPS-Ora-1288Ornithorhynchus anatinus88.73e-150 449
LLPS-Rhb-2836Rhinopithecus bieti87.370.01367
LLPS-Pes-3152Pelodiscus sinensis86.370.01458
LLPS-Tag-0779Taeniopygia guttata84.490.01428
LLPS-Anc-3706Anolis carolinensis83.660.01421
LLPS-Anp-3107Anas platyrhynchos83.60.01321
LLPS-Fia-3147Ficedula albicollis83.520.01327
LLPS-Gaga-3886Gallus gallus83.240.01399
LLPS-Meg-2272Meleagris gallopavo80.020.01266
LLPS-Aon-3428Aotus nancymaae77.790.01202
LLPS-Leo-0730Lepisosteus oculatus77.010.01299
LLPS-Lac-3711Latimeria chalumnae76.760.01325
LLPS-Dar-3364Danio rerio75.170.01301
LLPS-Scf-3187Scleropages formosus74.360.01280
LLPS-Icp-3331Ictalurus punctatus73.770.01285
LLPS-Xet-2235Xenopus tropicalis73.640.01244
LLPS-Asm-2645Astyanax mexicanus73.570.01268
LLPS-Ten-0969Tetraodon nigroviridis73.550.01248
LLPS-Pof-4105Poecilia formosa73.550.01258
LLPS-Tar-0955Takifugu rubripes72.330.01239
LLPS-Orl-2009Oryzias latipes72.160.01239
LLPS-Gaa-3461Gasterosteus aculeatus72.130.01222
LLPS-Xim-0536Xiphophorus maculatus72.010.01268
LLPS-Scm-2943Scophthalmus maximus71.990.01241
LLPS-Orn-1529Oreochromis niloticus71.980.01222
LLPS-Met-2594Medicago truncatula50.823e-1681.6
LLPS-Ori-1984Oryza indica48.216e-1062.8
LLPS-Cus-1867Cucumis sativus45.413e-97 315
LLPS-Viv-1345Vitis vinifera43.932e-22 100
LLPS-Hea-0007Helianthus annuus43.530.0 663
LLPS-Sem-1145Selaginella moellendorffii43.40.0 680
LLPS-Brn-3281Brassica napus43.160.0 658
LLPS-Bro-0193Brassica oleracea42.820.0 653
LLPS-Tra-0621Triticum aestivum42.670.0 663
LLPS-Nia-2373Nicotiana attenuata42.660.0 672
LLPS-Brr-2635Brassica rapa42.20.0 649
LLPS-Pot-2374Populus trichocarpa42.140.0 659
LLPS-Glm-2578Glycine max41.750.0 649
LLPS-Sei-0728Setaria italica41.480.0 622
LLPS-Mua-1258Musa acuminata38.660.0 605
LLPS-Coc-2315Corchorus capsularis38.526e-1682.0
LLPS-Mae-0456Manihot esculenta36.92e-163 503
LLPS-Cii-2135Ciona intestinalis29.929e-0653.9
LLPS-Scp-1353Schizosaccharomyces pombe28.84e-0655.1
LLPS-Phn-1173Phaeosphaeria nodorum28.489e-0756.6
LLPS-Cis-1504Ciona savignyi28.193e-0655.5
LLPS-Mal-1100Mandrillus leucophaeus26.61e-1379.3
LLPS-Miv-0869Microbotryum violaceum25.52e-0656.2
LLPS-Abg-1073Absidia glauca24.166e-1067.4
LLPS-Brd-1222Brachypodium distachyon21.623e-0655.1