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Q9NVE5

- UBP40_HUMAN

UniProt

Q9NVE5 - UBP40_HUMAN

Protein

Ubiquitin carboxyl-terminal hydrolase 40

Gene

USP40

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 107 (01 Oct 2014)
      Sequence version 3 (15 Feb 2005)
      Previous versions | rss
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    Functioni

    May be catalytically inactive.

    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 peptidase activity Source: UniProtKB-KW
    2. ubiquitinyl hydrolase activity Source: InterPro

    GO - Biological processi

    1. ubiquitin-dependent protein catabolic process Source: InterPro

    Keywords - Molecular functioni

    Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    Ubl conjugation pathway

    Protein family/group databases

    MEROPSiC19.069.

    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
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 2

    Organism-specific databases

    HGNCiHGNC:20069. USP40.

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA134909324.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 12351235Ubiquitin carboxyl-terminal hydrolase 40PRO_0000080670Add
    BLAST

    Proteomic databases

    MaxQBiQ9NVE5.
    PaxDbiQ9NVE5.
    PRIDEiQ9NVE5.

    PTM databases

    PhosphoSiteiQ9NVE5.

    Expressioni

    Tissue specificityi

    Broadly expressed.1 Publication

    Gene expression databases

    ArrayExpressiQ9NVE5.
    BgeeiQ9NVE5.
    CleanExiHS_USP40.
    GenevestigatoriQ9NVE5.

    Organism-specific databases

    HPAiHPA005821.

    Interactioni

    Protein-protein interaction databases

    BioGridi120525. 1 interaction.
    STRINGi9606.ENSP00000415434.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9NVE5.
    SMRiQ9NVE5. Positions 38-341.
    ModBaseiSearch...
    MobiDBiSearch...

    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.
    HOGENOMiHOG000154760.
    HOVERGENiHBG079302.
    InParanoidiQ9NVE5.
    KOiK11869.
    OMAiVWDLTFD.
    OrthoDBiEOG7R2BHT.
    PhylomeDBiQ9NVE5.
    TreeFamiTF106281.

    Family and domain databases

    InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028889. UCH/PAN2.
    [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 (3)i

    Sequence statusi: Complete.

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9NVE5-1) [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

    MFGDLFEEEY STVSNNQYGK GKKLKTKALE PPAPREFTNL SGIRNQGGTC     50
    YLNSLLQTLH FTPEFREALF SLGPEELGLF EDKDKPDAKV RIIPLQLQRL 100
    FAQLLLLDQE AASTADLTDS FGWTSNEEMR QHDVQELNRI LFSALETSLV 150
    GTSGHDLIYR LYHGTIVNQI VCKECKNVSE RQEDFLDLTV AVKNVSGLED 200
    ALWNMYVEEE VFDCDNLYHC GTCDRLVKAA KSAKLRKLPP FLTVSLLRFN 250
    FDFVKCERYK ETSCYTFPLR INLKPFCEQS ELDDLEYIYD LFSVIIHKGG 300
    CYGGHYHVYI KDVDHLGNWQ FQEEKSKPDV NLKDLQSEEE IDHPLMILKA 350
    ILLEENNLIP VDQLGQKLLK KIGISWNKKY RKQHGPLRKF LQLHSQIFLL 400
    SSDESTVRLL KNSSLQAESD FQRNDQQIFK MLPPESPGLN NSISCPHWFD 450
    INDSKVQPIR EKDIEQQFQG KESAYMLFYR KSQLQRPPEA RANPRYGVPC 500
    HLLNEMDAAN IELQTKRAEC DSANNTFELH LHLGPQYHFF NGALHPVVSQ 550
    TESVWDLTFD KRKTLGDLRQ SIFQLLEFWE GDMVLSVAKL VPAGLHIYQS 600
    LGGDELTLCE TEIADGEDIF VWNGVEVGGV HIQTGIDCEP LLLNVLHLDT 650
    SSDGEKCCQV IESPHVFPAN AEVGTVLTAL AIPAGVIFIN SAGCPGGEGW 700
    TAIPKEDMRK TFREQGLRNG SSILIQDSHD DNSLLTKEEK WVTSMNEIDW 750
    LHVKNLCQLE SEEKQVKISA TVNTMVFDIR IKAIKELKLM KELADNSCLR 800
    PIDRNGKLLC PVPDSYTLKE AELKMGSSLG LCLGKAPSSS QLFLFFAMGS 850
    DVQPGTEMEI VVEETISVRD CLKLMLKKSG LQGDAWHLRK MDWCYEAGEP 900
    LCEEDATLKE LLICSGDTLL LIEGQLPPLG FLKVPIWWYQ LQGPSGHWES 950
    HQDQTNCTSS WGRVWRATSS QGASGNEPAQ VSLLYLGDIE ISEDATLAEL 1000
    KSQAMTLPPF LEFGVPSPAH LRAWTVERKR PGRLLRTDRQ PLREYKLGRR 1050
    IEICLEPLQK GENLGPQDVL LRTQVRIPGE RTYAPALDLV WNAAQGGTAG 1100
    SLRQRVADFY RLPVEKIEIA KYFPEKFEWL PISSWNQQIT KRKKKKKQDY 1150
    LQGAPYYLKD GDTIGVKNLL IDDDDDFSTI RDDTGKEKQK QRALGRRKSQ 1200
    EALHEQSSYI LSSAETPARP RAPETSLSIH VGSFR 1235
    Length:1,235
    Mass (Da):140,130
    Last modified:February 15, 2005 - v3
    Checksum:iBEB20702566D39A8
    GO
    Isoform 2 (identifier: Q9NVE5-2) [UniParc]FASTAAdd to Basket

    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.

    Show »
    Length:163
    Mass (Da):18,298
    Checksum:i6DFD238BB2810182
    GO
    Isoform 3 (identifier: Q9NVE5-3) [UniParc]FASTAAdd to Basket

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

    Show »
    Length:1,247
    Mass (Da):141,558
    Checksum:iEB6B19218247C3FB
    GO

    Sequence cautioni

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

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti277 – 31842CEQSE…DHLGN → FFSFNQKMHNVCVNRRYGGS GMPLLRCGRCVGSAQPLSSV FR in AAH67300. (PubMed:15489334)CuratedAdd
    BLAST

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti666 – 6661V → A.
    Corresponds to variant rs838543 [ dbSNP | Ensembl ].
    VAR_017123
    Natural varianti1025 – 10251T → M.
    Corresponds to variant rs34026756 [ dbSNP | Ensembl ].
    VAR_059753
    Natural varianti1111 – 11111R → C.
    Corresponds to variant rs1048603 [ dbSNP | Ensembl ].
    VAR_017124

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 824824Missing in isoform 2. 1 PublicationVSP_008595Add
    BLAST
    Alternative sequencei1 – 11M → MSLFLRVVFSFTM in isoform 3. 1 PublicationVSP_040938
    Alternative sequencei973 – 98715ASGNE…LLYLG → ENRMGFQQPVHHKEK in isoform 2. 1 PublicationVSP_008596Add
    BLAST
    Alternative sequencei988 – 1235248Missing in isoform 2. 1 PublicationVSP_012819Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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.
    CCDSiCCDS46547.1. [Q9NVE5-3]
    RefSeqiNP_060688.1. NM_018218.2. [Q9NVE5-3]
    UniGeneiHs.96513.

    Genome annotation databases

    EnsembliENST00000251722; ENSP00000251722; ENSG00000085982. [Q9NVE5-1]
    ENST00000409945; ENSP00000386664; ENSG00000085982. [Q9NVE5-2]
    ENST00000427112; ENSP00000387898; ENSG00000085982. [Q9NVE5-1]
    ENST00000450966; ENSP00000415434; ENSG00000085982. [Q9NVE5-3]
    GeneIDi55230.
    KEGGihsa:55230.
    UCSCiuc002vuo.1. human. [Q9NVE5-2]
    uc010zmr.2. human. [Q9NVE5-3]

    Polymorphism databases

    DMDMi59803114.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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 .
    CCDSi CCDS46547.1. [Q9NVE5-3 ]
    RefSeqi NP_060688.1. NM_018218.2. [Q9NVE5-3 ]
    UniGenei Hs.96513.

    3D structure databases

    ProteinModelPortali Q9NVE5.
    SMRi Q9NVE5. Positions 38-341.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 120525. 1 interaction.
    STRINGi 9606.ENSP00000415434.

    Protein family/group databases

    MEROPSi C19.069.

    PTM databases

    PhosphoSitei Q9NVE5.

    Polymorphism databases

    DMDMi 59803114.

    Proteomic databases

    MaxQBi Q9NVE5.
    PaxDbi Q9NVE5.
    PRIDEi Q9NVE5.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000251722 ; ENSP00000251722 ; ENSG00000085982 . [Q9NVE5-1 ]
    ENST00000409945 ; ENSP00000386664 ; ENSG00000085982 . [Q9NVE5-2 ]
    ENST00000427112 ; ENSP00000387898 ; ENSG00000085982 . [Q9NVE5-1 ]
    ENST00000450966 ; ENSP00000415434 ; ENSG00000085982 . [Q9NVE5-3 ]
    GeneIDi 55230.
    KEGGi hsa:55230.
    UCSCi uc002vuo.1. human. [Q9NVE5-2 ]
    uc010zmr.2. human. [Q9NVE5-3 ]

    Organism-specific databases

    CTDi 55230.
    GeneCardsi GC02M234384.
    HGNCi HGNC:20069. USP40.
    HPAi HPA005821.
    MIMi 610570. gene.
    neXtProti NX_Q9NVE5.
    PharmGKBi PA134909324.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG5077.
    HOGENOMi HOG000154760.
    HOVERGENi HBG079302.
    InParanoidi Q9NVE5.
    KOi K11869.
    OMAi VWDLTFD.
    OrthoDBi EOG7R2BHT.
    PhylomeDBi Q9NVE5.
    TreeFami TF106281.

    Miscellaneous databases

    ChiTaRSi USP40. human.
    GeneWikii USP40.
    GenomeRNAii 55230.
    NextBioi 59237.
    PROi Q9NVE5.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9NVE5.
    Bgeei Q9NVE5.
    CleanExi HS_USP40.
    Genevestigatori Q9NVE5.

    Family and domain databases

    InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028889. UCH/PAN2.
    [Graphical view ]
    Pfami PF00443. UCH. 1 hit.
    [Graphical view ]
    PROSITEi PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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.

    Entry informationi

    Entry nameiUBP40_HUMAN
    AccessioniPrimary (citable) accession number: Q9NVE5
    Secondary accession number(s): Q6NX38, Q70EL0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 10, 2003
    Last sequence update: February 15, 2005
    Last modified: October 1, 2014
    This is version 107 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (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.

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 2
      Human chromosome 2: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. Peptidase families
      Classification of peptidase families and list of entries
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3