Q8BWR4 (UBP40_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:

Usp40

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	1235 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

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).
Sequence similarities	Belongs to the peptidase C19 family.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Coding sequence diversity	Alternative splicing
Molecular function	Hydrolase Protease Thiol protease
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro
Molecular_function	cysteine-type peptidase activity Inferred from electronic annotation. Source: UniProtKB-KW ubiquitin thiolesterase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q8BWR4-1)

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: Q8BWR4-2)

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

Note: No experimental confirmation available.

Isoform 3 (identifier: Q8BWR4-3)

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

Note: No experimental confirmation available.

Isoform 4 (identifier: Q8BWR4-4)

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

Note: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1235	1235	Ubiquitin carboxyl-terminal hydrolase 40		PRO_0000080671
Sites
	Active site	50	1	Nucleophile By similarity
	Active site	305	1	Proton acceptor By similarity
Amino acid modifications
	Modified residue	1207	1	Phosphoserine Ref.3
Natural variations
	Alternative sequence	1 – 128	128	Missing in isoform 3.		VSP_022171
	Alternative sequence	490 – 501	12	ARANP…RVPCH → GMENKKCSALLC in isoform 4.		VSP_022172
	Alternative sequence	502 – 1235	734	Missing in isoform 4.		VSP_022173
	Alternative sequence	795 – 883	89	Missing in isoform 2.		VSP_022174
Experimental info
	Sequence conflict	201	1	E → A in BAE38691. Ref.1
	Sequence conflict	943	1	A → E in AAH89376. Ref.2
	Sequence conflict	1134	1	S → N in BAE38411. Ref.1
	Sequence conflict	1142	1	R → K in AAH89376. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified January 9, 2007. Version 2. Checksum: CBAC7A6A0CACE03C	FASTA	1,235	139,952
	10 20 30 40 50 60 MFGNLFEEDY SSVSSSQYGR GKKLKTKGLE PPAPREFTNL SGIRNQGGTC YLSSLLQTLH 70 80 90 100 110 120 FTPEFREALF SLGPEELGSL EDKDKPDAKV RIIPLQLQRL FAQLLLLDQE AASTIDLTDS 130 140 150 160 170 180 FGWTNDEEMR QHDVQELNRI LFSALETSLV GTSGHDLIHR LYHGTIVNQI VCKECKNISE 190 200 210 220 230 240 RQEDFLDLTV AVKNVSGLED ELCNMYVEEE IFDYDNLYHC GTCDRLVKAA KSAKLRKLPP 250 260 270 280 290 300 FLTISLLRFN FDFVKCERYK DTSCYTFPLR INLKPFCEQS ELDDMEYMYD LFSVIIHKGG 310 320 330 340 350 360 CYGGHYHVYI KDVDHLGNWQ CQEEISDTNV NVKAPQSEEE ANDPLVVLKT ILLQEEANQI 370 380 390 400 410 420 PVDQLGQKLL KKTGISWNKK YRKQHGPLRK FLQLHPQIFL LSTDESTVSL LRNHLTQAPS 430 440 450 460 470 480 DLQSCEQILH TLASESPGLN DDTSCPHWFD INDSKVHPIR EKDITQQFQG KESAYMLFYR 490 500 510 520 530 540 KATLQRPPEA RANPRYRVPC HLLKEMDAAN ILLQMRRAEC DSANSTFELH LHLGPHYRFF 550 560 570 580 590 600 NGALHPAVSE TESVWDLTFD KRKTLGDLRQ SIFQLLECWE GDMVLSVAKR VPAGLHVYHT 610 620 630 640 650 660 LDGDDLTLCE AEVADGEDIF VWNGVEVGGV QIQTGFDCEP LLLNILHLEL SGEGSKCEQL 670 680 690 700 710 720 VESPHVFPAN AEVGAVFTAL GTPAGAILMN SVESADGECW TAVPKEDMKK TFREQGLRNG 730 740 750 760 770 780 SLILVQDSDS DNNSLLPKQG RWTNSMNELN WLQVKNFCQS ESEEKQVQIA VTMHTVVFDI 790 800 810 820 830 840 RIKAIKELKL MKELAENSCL RPIDRNGKLL CPVPDSSTLE EAEVKMGSSV GLCLGKAPTS 850 860 870 880 890 900 SQLFLFFALG TDIHPGAEMD IIVEETLSVR DCLKIMLEKS GQQGEIWHLR KMDWCYEAGE 910 920 930 940 950 960 PLCEEDATLK ELMIRSGDTL LLTEGKLPPP GHLKMPIWWY QPARLSGHCE SRDHLNCAFS 970 980 990 1000 1010 1020 QDSTWRAAPT QGAPGPEPAE VSLLYLGDME ISEEATLVEL KSQALALPSV SKLAVQSTAL 1030 1040 1050 1060 1070 1080 LRVWTVESKR PSRLLRTNWR QLKEYRLGRR AELCLELLQK EEDLGPRDVL LRTQLRIPGE 1090 1100 1110 1120 1130 1140 RAYSLATDLI WDTTRGWTAG SLRQRVADFY SLPVEKIEIA KYFPEKFEWL PISSWNQQVA 1150 1160 1170 1180 1190 1200 KRKKKKNQDT LQGGPYYLKD GDTIGIKNLL FDDNDDFSTI RDDIGKENQK RLALEKKKSR 1210 1220 1230 EVHRAQSSDL FSNAGVPARF RGPEASLSIH VASFR
	Isoform 2 [UniParc]. Checksum: 91974BE0E09AF9B5	FASTA	1,146	130,389
	10 20 30 40 50 60 MFGNLFEEDY SSVSSSQYGR GKKLKTKGLE PPAPREFTNL SGIRNQGGTC YLSSLLQTLH 70 80 90 100 110 120 FTPEFREALF SLGPEELGSL EDKDKPDAKV RIIPLQLQRL FAQLLLLDQE AASTIDLTDS 130 140 150 160 170 180 FGWTNDEEMR QHDVQELNRI LFSALETSLV GTSGHDLIHR LYHGTIVNQI VCKECKNISE 190 200 210 220 230 240 RQEDFLDLTV AVKNVSGLED ELCNMYVEEE IFDYDNLYHC GTCDRLVKAA KSAKLRKLPP 250 260 270 280 290 300 FLTISLLRFN FDFVKCERYK DTSCYTFPLR INLKPFCEQS ELDDMEYMYD LFSVIIHKGG 310 320 330 340 350 360 CYGGHYHVYI KDVDHLGNWQ CQEEISDTNV NVKAPQSEEE ANDPLVVLKT ILLQEEANQI 370 380 390 400 410 420 PVDQLGQKLL KKTGISWNKK YRKQHGPLRK FLQLHPQIFL LSTDESTVSL LRNHLTQAPS 430 440 450 460 470 480 DLQSCEQILH TLASESPGLN DDTSCPHWFD INDSKVHPIR EKDITQQFQG KESAYMLFYR 490 500 510 520 530 540 KATLQRPPEA RANPRYRVPC HLLKEMDAAN ILLQMRRAEC DSANSTFELH LHLGPHYRFF 550 560 570 580 590 600 NGALHPAVSE TESVWDLTFD KRKTLGDLRQ SIFQLLECWE GDMVLSVAKR VPAGLHVYHT 610 620 630 640 650 660 LDGDDLTLCE AEVADGEDIF VWNGVEVGGV QIQTGFDCEP LLLNILHLEL SGEGSKCEQL 670 680 690 700 710 720 VESPHVFPAN AEVGAVFTAL GTPAGAILMN SVESADGECW TAVPKEDMKK TFREQGLRNG 730 740 750 760 770 780 SLILVQDSDS DNNSLLPKQG RWTNSMNELN WLQVKNFCQS ESEEKQVQIA VTMHTVVFDI 790 800 810 820 830 840 RIKAIKELKL MKELGEIWHL RKMDWCYEAG EPLCEEDATL KELMIRSGDT LLLTEGKLPP 850 860 870 880 890 900 PGHLKMPIWW YQPARLSGHC ESRDHLNCAF SQDSTWRAAP TQGAPGPEPA EVSLLYLGDM 910 920 930 940 950 960 EISEEATLVE LKSQALALPS VSKLAVQSTA LLRVWTVESK RPSRLLRTNW RQLKEYRLGR 970 980 990 1000 1010 1020 RAELCLELLQ KEEDLGPRDV LLRTQLRIPG ERAYSLATDL IWDTTRGWTA GSLRQRVADF 1030 1040 1050 1060 1070 1080 YSLPVEKIEI AKYFPEKFEW LPISSWNQQV AKRKKKKNQD TLQGGPYYLK DGDTIGIKNL 1090 1100 1110 1120 1130 1140 LFDDNDDFST IRDDIGKENQ KRLALEKKKS REVHRAQSSD LFSNAGVPAR FRGPEASLSI HVASFR
	Isoform 3 [UniParc]. Checksum: F52FD5BAA6D8540A	FASTA	1,107	125,625
	10 20 30 40 50 60 MRQHDVQELN RILFSALETS LVGTSGHDLI HRLYHGTIVN QIVCKECKNI SERQEDFLDL 70 80 90 100 110 120 TVAVKNVSGL EDELCNMYVE EEIFDYDNLY HCGTCDRLVK AAKSAKLRKL PPFLTISLLR 130 140 150 160 170 180 FNFDFVKCER YKDTSCYTFP LRINLKPFCE QSELDDMEYM YDLFSVIIHK GGCYGGHYHV 190 200 210 220 230 240 YIKDVDHLGN WQCQEEISDT NVNVKAPQSE EEANDPLVVL KTILLQEEAN QIPVDQLGQK 250 260 270 280 290 300 LLKKTGISWN KKYRKQHGPL RKFLQLHPQI FLLSTDESTV SLLRNHLTQA PSDLQSCEQI 310 320 330 340 350 360 LHTLASESPG LNDDTSCPHW FDINDSKVHP IREKDITQQF QGKESAYMLF YRKATLQRPP 370 380 390 400 410 420 EARANPRYRV PCHLLKEMDA ANILLQMRRA ECDSANSTFE LHLHLGPHYR FFNGALHPAV 430 440 450 460 470 480 SETESVWDLT FDKRKTLGDL RQSIFQLLEC WEGDMVLSVA KRVPAGLHVY HTLDGDDLTL 490 500 510 520 530 540 CEAEVADGED IFVWNGVEVG GVQIQTGFDC EPLLLNILHL ELSGEGSKCE QLVESPHVFP 550 560 570 580 590 600 ANAEVGAVFT ALGTPAGAIL MNSVESADGE CWTAVPKEDM KKTFREQGLR NGSLILVQDS 610 620 630 640 650 660 DSDNNSLLPK QGRWTNSMNE LNWLQVKNFC QSESEEKQVQ IAVTMHTVVF DIRIKAIKEL 670 680 690 700 710 720 KLMKELAENS CLRPIDRNGK LLCPVPDSST LEEAEVKMGS SVGLCLGKAP TSSQLFLFFA 730 740 750 760 770 780 LGTDIHPGAE MDIIVEETLS VRDCLKIMLE KSGQQGEIWH LRKMDWCYEA GEPLCEEDAT 790 800 810 820 830 840 LKELMIRSGD TLLLTEGKLP PPGHLKMPIW WYQPARLSGH CESRDHLNCA FSQDSTWRAA 850 860 870 880 890 900 PTQGAPGPEP AEVSLLYLGD MEISEEATLV ELKSQALALP SVSKLAVQST ALLRVWTVES 910 920 930 940 950 960 KRPSRLLRTN WRQLKEYRLG RRAELCLELL QKEEDLGPRD VLLRTQLRIP GERAYSLATD 970 980 990 1000 1010 1020 LIWDTTRGWT AGSLRQRVAD FYSLPVEKIE IAKYFPEKFE WLPISSWNQQ VAKRKKKKNQ 1030 1040 1050 1060 1070 1080 DTLQGGPYYL KDGDTIGIKN LLFDDNDDFS TIRDDIGKEN QKRLALEKKK SREVHRAQSS 1090 1100 DLFSNAGVPA RFRGPEASLS IHVASFR
	Isoform 4 [UniParc]. Checksum: DB8DAE538B27B9EB	FASTA	501	57,394
	10 20 30 40 50 60 MFGNLFEEDY SSVSSSQYGR GKKLKTKGLE PPAPREFTNL SGIRNQGGTC YLSSLLQTLH 70 80 90 100 110 120 FTPEFREALF SLGPEELGSL EDKDKPDAKV RIIPLQLQRL FAQLLLLDQE AASTIDLTDS 130 140 150 160 170 180 FGWTNDEEMR QHDVQELNRI LFSALETSLV GTSGHDLIHR LYHGTIVNQI VCKECKNISE 190 200 210 220 230 240 RQEDFLDLTV AVKNVSGLED ELCNMYVEEE IFDYDNLYHC GTCDRLVKAA KSAKLRKLPP 250 260 270 280 290 300 FLTISLLRFN FDFVKCERYK DTSCYTFPLR INLKPFCEQS ELDDMEYMYD LFSVIIHKGG 310 320 330 340 350 360 CYGGHYHVYI KDVDHLGNWQ CQEEISDTNV NVKAPQSEEE ANDPLVVLKT ILLQEEANQI 370 380 390 400 410 420 PVDQLGQKLL KKTGISWNKK YRKQHGPLRK FLQLHPQIFL LSTDESTVSL LRNHLTQAPS 430 440 450 460 470 480 DLQSCEQILH TLASESPGLN DDTSCPHWFD INDSKVHPIR EKDITQQFQG KESAYMLFYR 490 500 KATLQRPPEG MENKKCSALL C

References

[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]	"Large-scale phosphorylation analysis of mouse liver." Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1207, MASS SPECTROMETRY. Tissue: Liver.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
IPI	IPI00761550. IPI00816992. IPI00817031. IPI00817048.
RefSeq	NP_001028463.1. NM_001033291.2. NP_001185502.1. NM_001198573.1.
UniGene	Mm.80484.
3D structure databases
ProteinModelPortal	Q8BWR4.
SMR	Q8BWR4. Positions 35-310.
ModBase	Search...
Protein-protein interaction databases
MINT	MINT-4139230.
Protein family/group databases
MEROPS	C19.069.
PTM databases
PhosphoSite	Q8BWR4.
Proteomic databases
PaxDb	Q8BWR4.
PRIDE	Q8BWR4.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000040783; ENSMUSP00000038533; ENSMUSG00000005501.
GeneID	227334.
KEGG	mmu:227334.
UCSC	uc007bxw.1. mouse. uc007bxx.1. mouse. uc007bxz.1. mouse.
Organism-specific databases
CTD	55230.
MGI	MGI:2443184. Usp40.
Phylogenomic databases
eggNOG	COG5077.
GeneTree	ENSGT00630000089581.
HOVERGEN	HBG079302.
InParanoid	Q8BWR4.
KO	K11869.
OMA	NLKPFCE.
OrthoDB	EOG4PVNXZ.
Gene expression databases
Bgee	Q8BWR4.
CleanEx	MM_USP40.
Genevestigator	Q8BWR4.
Family and domain databases
InterPro	IPR018200. Pept_C19ubi-hydrolase_C_CS. IPR001394. Peptidase_C19. [Graphical view]
Pfam	PF00443. UCH. 1 hit. [Graphical view]
PROSITE	PS00972. UCH_2_1. 1 hit. PS00973. UCH_2_2. 1 hit. PS50235. UCH_2_3. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	378568.
SOURCE	Search...

Entry information

Entry name

UBP40_MOUSE

Accession

Primary (citable) accession number: Q8BWR4
Secondary accession number(s): Q08EB7 , Q148V0, Q3TLV1, Q3TMN0, Q3V1R4, Q5EBN6

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 10, 2003
Last sequence update:	January 9, 2007
Last modified:	May 29, 2013
This is version 80 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program