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Q9NVE5 (UBP40_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 102. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1235 AA.
Sequence statusComplete.
Protein existenceEvidence 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.

Contains 1 USP domain.

Sequence caution

The sequence BAA91807.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
   Biological processUbl conjugation pathway
   Coding sequence diversityAlternative splicing
Polymorphism
   Molecular functionHydrolase
Protease
Thiol protease
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processubiquitin-dependent protein catabolic process

Inferred from electronic annotation. Source: InterPro

   Molecular_functioncysteine-type peptidase activity

Inferred from electronic annotation. Source: UniProtKB-KW

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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 12351235Ubiquitin carboxyl-terminal hydrolase 40
PRO_0000080670

Regions

Domain41 – 482442USP

Sites

Active site501Nucleophile By similarity
Active site3051Proton acceptor By similarity

Natural variations

Alternative sequence1 – 824824Missing in isoform 2.
VSP_008595
Alternative sequence11M → MSLFLRVVFSFTM in isoform 3.
VSP_040938
Alternative sequence973 – 98715ASGNE…LLYLG → ENRMGFQQPVHHKEK in isoform 2.
VSP_008596
Alternative sequence988 – 1235248Missing in isoform 2.
VSP_012819
Natural variant6661V → A.
Corresponds to variant rs838543 [ dbSNP | Ensembl ].
VAR_017123
Natural variant10251T → M.
Corresponds to variant rs34026756 [ dbSNP | Ensembl ].
VAR_059753
Natural variant11111R → C.
Corresponds to variant rs1048603 [ dbSNP | Ensembl ].
VAR_017124

Experimental info

Sequence conflict277 – 31842CEQSE…DHLGN → FFSFNQKMHNVCVNRRYGGS GMPLLRCGRCVGSAQPLSSV FR in AAH67300. Ref.4

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified February 15, 2005. Version 3.
Checksum: BEB20702566D39A8

FASTA1,235140,130
        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 

« Hide

Isoform 2 [UniParc].

Checksum: 6DFD238BB2810182
Show »

FASTA16318,298
Isoform 3 [UniParc].

Checksum: EB6B19218247C3FB
Show »

FASTA1,247141,558

References

« Hide '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. expand/collapse author list , 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. expand/collapse author list , 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.
RefSeqNP_060688.1. NM_018218.2.
UniGeneHs.96513.

3D structure databases

ProteinModelPortalQ9NVE5.
SMRQ9NVE5. Positions 35-512, 857-921.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid120525. 1 interaction.
STRING9606.ENSP00000415434.

Protein family/group databases

MEROPSC19.069.

PTM databases

PhosphoSiteQ9NVE5.

Polymorphism databases

DMDM59803114.

Proteomic databases

PaxDbQ9NVE5.
PRIDEQ9NVE5.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000251722; ENSP00000251722; ENSG00000085982. [Q9NVE5-1]
ENST00000409945; ENSP00000386664; ENSG00000085982. [Q9NVE5-2]
ENST00000427112; ENSP00000387898; ENSG00000085982. [Q9NVE5-1]
ENST00000450966; ENSP00000415434; ENSG00000085982. [Q9NVE5-3]
GeneID55230.
KEGGhsa:55230.
UCSCuc002vuo.1. human. [Q9NVE5-2]
uc010zmr.2. human. [Q9NVE5-3]

Organism-specific databases

CTD55230.
GeneCardsGC02M234384.
HGNCHGNC:20069. USP40.
HPAHPA005821.
MIM610570. gene.
neXtProtNX_Q9NVE5.
PharmGKBPA134909324.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5077.
HOGENOMHOG000154760.
HOVERGENHBG079302.
InParanoidQ9NVE5.
KOK11869.
OMAVWDLTFD.
OrthoDBEOG7R2BHT.
PhylomeDBQ9NVE5.
TreeFamTF106281.

Gene expression databases

ArrayExpressQ9NVE5.
BgeeQ9NVE5.
CleanExHS_USP40.
GenevestigatorQ9NVE5.

Family and domain databases

InterProIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
[Graphical view]
PfamPF00443. UCH. 1 hit.
[Graphical view]
PROSITEPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSUSP40. human.
GeneWikiUSP40.
GenomeRNAi55230.
NextBio59237.
PROQ9NVE5.
SOURCESearch...

Entry information

Entry nameUBP40_HUMAN
AccessionPrimary (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: April 16, 2014
This is version 102 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM