Q9NVE5 (UBP40_HUMAN) 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

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

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

General annotation (Comments)

Function	May be catalytically inactive.
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). Ref.1
Tissue specificity	Broadly expressed. Ref.1
Sequence similarities	Belongs to the peptidase C19 family.
Sequence caution	The sequence BAA91807.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Coding sequence diversity	Alternative splicing Polymorphism
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 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q9NVE5-1)

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: Q9NVE5-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-824: Missing.
     973-987: ASGNEPAQVSLLYLG → ENRMGFQQPVHHKEK
     988-1235: Missing.

Note: No experimental confirmation available.

Isoform 3 (identifier: Q9NVE5-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MSLFLRVVFSFTM

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_0000080670
Sites
	Active site	50	1	Nucleophile By similarity
	Active site	305	1	Proton acceptor By similarity
Amino acid modifications
	Modified residue	1207	1	Phosphoserine By similarity
Natural variations
	Alternative sequence	1 – 824	824	Missing in isoform 2.		VSP_008595
	Alternative sequence	1	1	M → MSLFLRVVFSFTM in isoform 3.		VSP_040938
	Alternative sequence	973 – 987	15	ASGNE…LLYLG → ENRMGFQQPVHHKEK in isoform 2.		VSP_008596
	Alternative sequence	988 – 1235	248	Missing in isoform 2.		VSP_012819
	Natural variant	666	1	V → A. Corresponds to variant rs838543 [ dbSNP | Ensembl ].		VAR_017123
	Natural variant	1025	1	T → M. Corresponds to variant rs34026756 [ dbSNP | Ensembl ].		VAR_059753
	Natural variant	1111	1	R → C. Corresponds to variant rs1048603 [ dbSNP | Ensembl ].		VAR_017124
Experimental info
	Sequence conflict	277 – 318	42	CEQSE…DHLGN → FFSFNQKMHNVCVNRRYGGS GMPLLRCGRCVGSAQPLSSV FR in AAH67300. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified February 15, 2005. Version 3. Checksum: BEB20702566D39A8	FASTA	1,235	140,130
	10 20 30 40 50 60 MFGDLFEEEY STVSNNQYGK GKKLKTKALE PPAPREFTNL SGIRNQGGTC YLNSLLQTLH 70 80 90 100 110 120 FTPEFREALF SLGPEELGLF EDKDKPDAKV RIIPLQLQRL FAQLLLLDQE AASTADLTDS 130 140 150 160 170 180 FGWTSNEEMR QHDVQELNRI LFSALETSLV GTSGHDLIYR LYHGTIVNQI VCKECKNVSE 190 200 210 220 230 240 RQEDFLDLTV AVKNVSGLED ALWNMYVEEE VFDCDNLYHC GTCDRLVKAA KSAKLRKLPP 250 260 270 280 290 300 FLTVSLLRFN FDFVKCERYK ETSCYTFPLR INLKPFCEQS ELDDLEYIYD LFSVIIHKGG 310 320 330 340 350 360 CYGGHYHVYI KDVDHLGNWQ FQEEKSKPDV NLKDLQSEEE IDHPLMILKA ILLEENNLIP 370 380 390 400 410 420 VDQLGQKLLK KIGISWNKKY RKQHGPLRKF LQLHSQIFLL SSDESTVRLL KNSSLQAESD 430 440 450 460 470 480 FQRNDQQIFK MLPPESPGLN NSISCPHWFD INDSKVQPIR EKDIEQQFQG KESAYMLFYR 490 500 510 520 530 540 KSQLQRPPEA RANPRYGVPC HLLNEMDAAN IELQTKRAEC DSANNTFELH LHLGPQYHFF 550 560 570 580 590 600 NGALHPVVSQ TESVWDLTFD KRKTLGDLRQ SIFQLLEFWE GDMVLSVAKL VPAGLHIYQS 610 620 630 640 650 660 LGGDELTLCE TEIADGEDIF VWNGVEVGGV HIQTGIDCEP LLLNVLHLDT SSDGEKCCQV 670 680 690 700 710 720 IESPHVFPAN AEVGTVLTAL AIPAGVIFIN SAGCPGGEGW TAIPKEDMRK TFREQGLRNG 730 740 750 760 770 780 SSILIQDSHD DNSLLTKEEK WVTSMNEIDW LHVKNLCQLE SEEKQVKISA TVNTMVFDIR 790 800 810 820 830 840 IKAIKELKLM KELADNSCLR PIDRNGKLLC PVPDSYTLKE AELKMGSSLG LCLGKAPSSS 850 860 870 880 890 900 QLFLFFAMGS DVQPGTEMEI VVEETISVRD CLKLMLKKSG LQGDAWHLRK MDWCYEAGEP 910 920 930 940 950 960 LCEEDATLKE LLICSGDTLL LIEGQLPPLG FLKVPIWWYQ LQGPSGHWES HQDQTNCTSS 970 980 990 1000 1010 1020 WGRVWRATSS QGASGNEPAQ VSLLYLGDIE ISEDATLAEL KSQAMTLPPF LEFGVPSPAH 1030 1040 1050 1060 1070 1080 LRAWTVERKR PGRLLRTDRQ PLREYKLGRR IEICLEPLQK GENLGPQDVL LRTQVRIPGE 1090 1100 1110 1120 1130 1140 RTYAPALDLV WNAAQGGTAG SLRQRVADFY RLPVEKIEIA KYFPEKFEWL PISSWNQQIT 1150 1160 1170 1180 1190 1200 KRKKKKKQDY LQGAPYYLKD GDTIGVKNLL IDDDDDFSTI RDDTGKEKQK QRALGRRKSQ 1210 1220 1230 EALHEQSSYI LSSAETPARP RAPETSLSIH VGSFR
	Isoform 2 [UniParc]. Checksum: 6DFD238BB2810182	FASTA	163	18,298
	10 20 30 40 50 60 MGSSLGLCLG KAPSSSQLFL FFAMGSDVQP GTEMEIVVEE TISVRDCLKL MLKKSGLQGD 70 80 90 100 110 120 AWHLRKMDWC YEAGEPLCEE DATLKELLIC SGDTLLLIEG QLPPLGFLKV PIWWYQLQGP 130 140 150 160 SGHWESHQDQ TNCTSSWGRV WRATSSQGEN RMGFQQPVHH KEK
	Isoform 3 [UniParc]. Checksum: EB6B19218247C3FB	FASTA	1,247	141,558
	10 20 30 40 50 60 MSLFLRVVFS FTMFGDLFEE EYSTVSNNQY GKGKKLKTKA LEPPAPREFT NLSGIRNQGG 70 80 90 100 110 120 TCYLNSLLQT LHFTPEFREA LFSLGPEELG LFEDKDKPDA KVRIIPLQLQ RLFAQLLLLD 130 140 150 160 170 180 QEAASTADLT DSFGWTSNEE MRQHDVQELN RILFSALETS LVGTSGHDLI YRLYHGTIVN 190 200 210 220 230 240 QIVCKECKNV SERQEDFLDL TVAVKNVSGL EDALWNMYVE EEVFDCDNLY HCGTCDRLVK 250 260 270 280 290 300 AAKSAKLRKL PPFLTVSLLR FNFDFVKCER YKETSCYTFP LRINLKPFCE QSELDDLEYI 310 320 330 340 350 360 YDLFSVIIHK GGCYGGHYHV YIKDVDHLGN WQFQEEKSKP DVNLKDLQSE EEIDHPLMIL 370 380 390 400 410 420 KAILLEENNL IPVDQLGQKL LKKIGISWNK KYRKQHGPLR KFLQLHSQIF LLSSDESTVR 430 440 450 460 470 480 LLKNSSLQAE SDFQRNDQQI FKMLPPESPG LNNSISCPHW FDINDSKVQP IREKDIEQQF 490 500 510 520 530 540 QGKESAYMLF YRKSQLQRPP EARANPRYGV PCHLLNEMDA ANIELQTKRA ECDSANNTFE 550 560 570 580 590 600 LHLHLGPQYH FFNGALHPVV SQTESVWDLT FDKRKTLGDL RQSIFQLLEF WEGDMVLSVA 610 620 630 640 650 660 KLVPAGLHIY QSLGGDELTL CETEIADGED IFVWNGVEVG GVHIQTGIDC EPLLLNVLHL 670 680 690 700 710 720 DTSSDGEKCC QVIESPHVFP ANAEVGTVLT ALAIPAGVIF INSAGCPGGE GWTAIPKEDM 730 740 750 760 770 780 RKTFREQGLR NGSSILIQDS HDDNSLLTKE EKWVTSMNEI DWLHVKNLCQ LESEEKQVKI 790 800 810 820 830 840 SATVNTMVFD IRIKAIKELK LMKELADNSC LRPIDRNGKL LCPVPDSYTL KEAELKMGSS 850 860 870 880 890 900 LGLCLGKAPS SSQLFLFFAM GSDVQPGTEM EIVVEETISV RDCLKLMLKK SGLQGDAWHL 910 920 930 940 950 960 RKMDWCYEAG EPLCEEDATL KELLICSGDT LLLIEGQLPP LGFLKVPIWW YQLQGPSGHW 970 980 990 1000 1010 1020 ESHQDQTNCT SSWGRVWRAT SSQGASGNEP AQVSLLYLGD IEISEDATLA ELKSQAMTLP 1030 1040 1050 1060 1070 1080 PFLEFGVPSP AHLRAWTVER KRPGRLLRTD RQPLREYKLG RRIEICLEPL QKGENLGPQD 1090 1100 1110 1120 1130 1140 VLLRTQVRIP GERTYAPALD LVWNAAQGGT AGSLRQRVAD FYRLPVEKIE IAKYFPEKFE 1150 1160 1170 1180 1190 1200 WLPISSWNQQ ITKRKKKKKQ DYLQGAPYYL KDGDTIGVKN LLIDDDDDFS TIRDDTGKEK 1210 1220 1230 1240 QKQRALGRRK SQEALHEQSS YILSSAETPA RPRAPETSLS IHVGSFR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and enzymatic analysis of 22 novel human ubiquitin-specific proteases." Quesada V., Diaz-Perales A., Gutierrez-Fernandez A., Garabaya C., Cal S., Lopez-Otin C. Biochem. Biophys. Res. Commun. 314:54-62(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), LACK OF ENZYME ACTIVITY, TISSUE SPECIFICITY.
[2]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 2-1142 (ISOFORM 1). Tissue: Esophagus and Teratocarcinoma.
[3]	"Generation and annotation of the DNA sequences of human chromosomes 2 and 4." Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K. Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"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 1-318 (ISOFORM 1). Tissue: Testis.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AJ583821 mRNA. Translation: CAE47748.2. AK001647 mRNA. Translation: BAA91807.1. Different initiation. AK124094 mRNA. Translation: BAC85770.1. AC019221 Genomic DNA. No translation available. AC019072 Genomic DNA. No translation available. BC067300 mRNA. Translation: AAH67300.1.
IPI	IPI00373874. IPI00398007. IPI00947085.
RefSeq	NP_060688.1. NM_018218.2.
UniGene	Hs.96513.
3D structure databases
ProteinModelPortal	Q9NVE5.
ModBase	Search...
Protein-protein interaction databases
STRING	9606.ENSP00000415434.
Protein family/group databases
MEROPS	C19.069.
PTM databases
PhosphoSite	Q9NVE5.
Polymorphism databases
DMDM	59803114.
Proteomic databases
PaxDb	Q9NVE5.
PRIDE	Q9NVE5.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000251722; ENSP00000251722; ENSG00000085982. ENST00000409945; ENSP00000386664; ENSG00000085982. ENST00000427112; ENSP00000387898; ENSG00000085982. ENST00000450966; ENSP00000415434; ENSG00000085982.
GeneID	55230.
KEGG	hsa:55230.
UCSC	uc002vuo.1. human. uc010zmr.2. human.
Organism-specific databases
CTD	55230.
GeneCards	GC02M234384.
HGNC	HGNC:20069. USP40.
HPA	HPA005821.
MIM	610570. gene.
neXtProt	NX_Q9NVE5.
PharmGKB	PA134909324.
GenAtlas	Search...
Phylogenomic databases
eggNOG	COG5077.
HOGENOM	HOG000154760.
HOVERGEN	HBG079302.
InParanoid	Q9NVE5.
KO	K11869.
OMA	NLKPFCE.
OrthoDB	EOG4PVNXZ.
Gene expression databases
ArrayExpress	Q9NVE5.
Bgee	Q9NVE5.
CleanEx	HS_USP40.
Genevestigator	Q9NVE5.
GermOnline	ENSG00000085982. Homo sapiens.
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
ChiTaRS	USP40. human.
GenomeRNAi	55230.
NextBio	59237.
SOURCE	Search...

Entry information

Entry name

UBP40_HUMAN

Accession

Primary (citable) accession number: Q9NVE5
Secondary accession number(s): Q6NX38, Q70EL0

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 10, 2003
Last sequence update:	February 15, 2005
Last modified:	May 1, 2013
This is version 94 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.