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Protein

Ubiquitin carboxyl-terminal hydrolase 40

Gene

Usp40

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

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).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei50 – 501NucleophilePROSITE-ProRule annotation
Active sitei305 – 3051Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

  1. cysteine-type endopeptidase activity Source: GO_Central
  2. ubiquitin-specific protease activity Source: GO_Central
  3. ubiquitin thiolesterase activity Source: GO_Central

GO - Biological processi

  1. proteasome-mediated ubiquitin-dependent protein catabolic process Source: GO_Central
  2. protein deubiquitination Source: GO_Central
  3. regulation of proteasomal protein catabolic process Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase 40 (EC:3.4.19.12)
Alternative name(s):
Deubiquitinating enzyme 40
Ubiquitin thioesterase 40
Ubiquitin-specific-processing protease 40
Gene namesi
Name:Usp40
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 1

Organism-specific databases

MGIiMGI:2443184. Usp40.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: GO_Central
  2. nucleus Source: GO_Central
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12351235Ubiquitin carboxyl-terminal hydrolase 40PRO_0000080671Add
BLAST

Proteomic databases

MaxQBiQ8BWR4.
PaxDbiQ8BWR4.
PRIDEiQ8BWR4.

PTM databases

PhosphoSiteiQ8BWR4.

Expressioni

Gene expression databases

BgeeiQ8BWR4.
CleanExiMM_USP40.
GenevestigatoriQ8BWR4.

Interactioni

Protein-protein interaction databases

IntActiQ8BWR4. 1 interaction.
MINTiMINT-4139230.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini41 – 482442USPAdd
BLAST

Sequence similaritiesi

Belongs to the peptidase C19 family.Curated
Contains 1 USP domain.Curated

Phylogenomic databases

eggNOGiCOG5077.
GeneTreeiENSGT00760000119158.
HOVERGENiHBG079302.
InParanoidiQ8BWR4.
KOiK11869.
OMAiVWDLTFD.
OrthoDBiEOG7R2BHT.
PhylomeDBiQ8BWR4.
TreeFamiTF106281.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
[Graphical view]
PfamiPF00443. UCH. 1 hit.
[Graphical view]
PROSITEiPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q8BWR4-1) [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
MFGNLFEEDY SSVSSSQYGR GKKLKTKGLE PPAPREFTNL SGIRNQGGTC
60 70 80 90 100
YLSSLLQTLH FTPEFREALF SLGPEELGSL EDKDKPDAKV RIIPLQLQRL
110 120 130 140 150
FAQLLLLDQE AASTIDLTDS FGWTNDEEMR QHDVQELNRI LFSALETSLV
160 170 180 190 200
GTSGHDLIHR LYHGTIVNQI VCKECKNISE RQEDFLDLTV AVKNVSGLED
210 220 230 240 250
ELCNMYVEEE IFDYDNLYHC GTCDRLVKAA KSAKLRKLPP FLTISLLRFN
260 270 280 290 300
FDFVKCERYK DTSCYTFPLR INLKPFCEQS ELDDMEYMYD LFSVIIHKGG
310 320 330 340 350
CYGGHYHVYI KDVDHLGNWQ CQEEISDTNV NVKAPQSEEE ANDPLVVLKT
360 370 380 390 400
ILLQEEANQI PVDQLGQKLL KKTGISWNKK YRKQHGPLRK FLQLHPQIFL
410 420 430 440 450
LSTDESTVSL LRNHLTQAPS DLQSCEQILH TLASESPGLN DDTSCPHWFD
460 470 480 490 500
INDSKVHPIR EKDITQQFQG KESAYMLFYR KATLQRPPEA RANPRYRVPC
510 520 530 540 550
HLLKEMDAAN ILLQMRRAEC DSANSTFELH LHLGPHYRFF NGALHPAVSE
560 570 580 590 600
TESVWDLTFD KRKTLGDLRQ SIFQLLECWE GDMVLSVAKR VPAGLHVYHT
610 620 630 640 650
LDGDDLTLCE AEVADGEDIF VWNGVEVGGV QIQTGFDCEP LLLNILHLEL
660 670 680 690 700
SGEGSKCEQL VESPHVFPAN AEVGAVFTAL GTPAGAILMN SVESADGECW
710 720 730 740 750
TAVPKEDMKK TFREQGLRNG SLILVQDSDS DNNSLLPKQG RWTNSMNELN
760 770 780 790 800
WLQVKNFCQS ESEEKQVQIA VTMHTVVFDI RIKAIKELKL MKELAENSCL
810 820 830 840 850
RPIDRNGKLL CPVPDSSTLE EAEVKMGSSV GLCLGKAPTS SQLFLFFALG
860 870 880 890 900
TDIHPGAEMD IIVEETLSVR DCLKIMLEKS GQQGEIWHLR KMDWCYEAGE
910 920 930 940 950
PLCEEDATLK ELMIRSGDTL LLTEGKLPPP GHLKMPIWWY QPARLSGHCE
960 970 980 990 1000
SRDHLNCAFS QDSTWRAAPT QGAPGPEPAE VSLLYLGDME ISEEATLVEL
1010 1020 1030 1040 1050
KSQALALPSV SKLAVQSTAL LRVWTVESKR PSRLLRTNWR QLKEYRLGRR
1060 1070 1080 1090 1100
AELCLELLQK EEDLGPRDVL LRTQLRIPGE RAYSLATDLI WDTTRGWTAG
1110 1120 1130 1140 1150
SLRQRVADFY SLPVEKIEIA KYFPEKFEWL PISSWNQQVA KRKKKKNQDT
1160 1170 1180 1190 1200
LQGGPYYLKD GDTIGIKNLL FDDNDDFSTI RDDIGKENQK RLALEKKKSR
1210 1220 1230
EVHRAQSSDL FSNAGVPARF RGPEASLSIH VASFR
Length:1,235
Mass (Da):139,952
Last modified:January 9, 2007 - v2
Checksum:iCBAC7A6A0CACE03C
GO
Isoform 2 (identifier: Q8BWR4-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     795-883: Missing.

Note: No experimental confirmation available.

Show »
Length:1,146
Mass (Da):130,389
Checksum:i91974BE0E09AF9B5
GO
Isoform 3 (identifier: Q8BWR4-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-128: Missing.

Note: No experimental confirmation available.

Show »
Length:1,107
Mass (Da):125,625
Checksum:iF52FD5BAA6D8540A
GO
Isoform 4 (identifier: Q8BWR4-4) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     490-501: ARANPRYRVPCH → GMENKKCSALLC
     502-1235: Missing.

Note: No experimental confirmation available.

Show »
Length:501
Mass (Da):57,394
Checksum:iDB8DAE538B27B9EB
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti201 – 2011E → A in BAE38691. (PubMed:16141072)Curated
Sequence conflicti943 – 9431A → E in AAH89376. (PubMed:15489334)Curated
Sequence conflicti1134 – 11341S → N in BAE38411. (PubMed:16141072)Curated
Sequence conflicti1142 – 11421R → K in AAH89376. (PubMed:15489334)Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 128128Missing in isoform 3. 1 PublicationVSP_022171Add
BLAST
Alternative sequencei490 – 50112ARANP…RVPCH → GMENKKCSALLC in isoform 4. 1 PublicationVSP_022172Add
BLAST
Alternative sequencei502 – 1235734Missing in isoform 4. 1 PublicationVSP_022173Add
BLAST
Alternative sequencei795 – 88389Missing in isoform 2. 1 PublicationVSP_022174Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK050239 mRNA. Translation: BAC34140.1.
AK132295 mRNA. Translation: BAE21086.1.
AK165849 mRNA. Translation: BAE38411.1.
AK166303 mRNA. Translation: BAE38691.1.
BC089376 mRNA. Translation: AAH89376.1.
BC117957 mRNA. Translation: AAI17958.1.
BC117958 mRNA. Translation: AAI17959.1.
CCDSiCCDS15137.1. [Q8BWR4-2]
RefSeqiNP_001028463.1. NM_001033291.2. [Q8BWR4-2]
NP_001185502.1. NM_001198573.1. [Q8BWR4-1]
XP_006529542.1. XM_006529479.1. [Q8BWR4-3]
UniGeneiMm.80484.

Genome annotation databases

EnsembliENSMUST00000040783; ENSMUSP00000038533; ENSMUSG00000005501. [Q8BWR4-2]
ENSMUST00000187758; ENSMUSP00000140107; ENSMUSG00000005501. [Q8BWR4-1]
GeneIDi227334.
KEGGimmu:227334.
UCSCiuc007bxw.1. mouse. [Q8BWR4-2]
uc007bxx.1. mouse. [Q8BWR4-1]
uc007bxz.1. mouse. [Q8BWR4-4]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK050239 mRNA. Translation: BAC34140.1.
AK132295 mRNA. Translation: BAE21086.1.
AK165849 mRNA. Translation: BAE38411.1.
AK166303 mRNA. Translation: BAE38691.1.
BC089376 mRNA. Translation: AAH89376.1.
BC117957 mRNA. Translation: AAI17958.1.
BC117958 mRNA. Translation: AAI17959.1.
CCDSiCCDS15137.1. [Q8BWR4-2]
RefSeqiNP_001028463.1. NM_001033291.2. [Q8BWR4-2]
NP_001185502.1. NM_001198573.1. [Q8BWR4-1]
XP_006529542.1. XM_006529479.1. [Q8BWR4-3]
UniGeneiMm.80484.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ8BWR4. 1 interaction.
MINTiMINT-4139230.

PTM databases

PhosphoSiteiQ8BWR4.

Proteomic databases

MaxQBiQ8BWR4.
PaxDbiQ8BWR4.
PRIDEiQ8BWR4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000040783; ENSMUSP00000038533; ENSMUSG00000005501. [Q8BWR4-2]
ENSMUST00000187758; ENSMUSP00000140107; ENSMUSG00000005501. [Q8BWR4-1]
GeneIDi227334.
KEGGimmu:227334.
UCSCiuc007bxw.1. mouse. [Q8BWR4-2]
uc007bxx.1. mouse. [Q8BWR4-1]
uc007bxz.1. mouse. [Q8BWR4-4]

Organism-specific databases

CTDi55230.
MGIiMGI:2443184. Usp40.

Phylogenomic databases

eggNOGiCOG5077.
GeneTreeiENSGT00760000119158.
HOVERGENiHBG079302.
InParanoidiQ8BWR4.
KOiK11869.
OMAiVWDLTFD.
OrthoDBiEOG7R2BHT.
PhylomeDBiQ8BWR4.
TreeFamiTF106281.

Miscellaneous databases

ChiTaRSiUsp40. mouse.
NextBioi378568.
PROiQ8BWR4.
SOURCEiSearch...

Gene expression databases

BgeeiQ8BWR4.
CleanExiMM_USP40.
GenevestigatoriQ8BWR4.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
[Graphical view]
PfamiPF00443. UCH. 1 hit.
[Graphical view]
PROSITEiPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 4), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-1140 AND 967-1235 (ISOFORM 1).
    Strain: C57BL/6J.
    Tissue: Embryo, Liver, Lung and Mammary gland.
  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] (ISOFORMS 1 AND 3).
    Strain: C57BL/6.
    Tissue: Eye.
  3. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.

Entry informationi

Entry nameiUBP40_MOUSE
AccessioniPrimary (citable) accession number: Q8BWR4
Secondary accession number(s): Q08EB7
, Q148V0, Q3TLV1, Q3TMN0, Q3V1R4, Q5EBN6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2003
Last sequence update: January 9, 2007
Last modified: February 4, 2015
This is version 96 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. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.