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Q9NVE5

- UBP40_HUMAN

UniProt

Q9NVE5 - UBP40_HUMAN

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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

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
Complete GO annotation...

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

BgeeiQ9NVE5.
CleanExiHS_USP40.
ExpressionAtlasiQ9NVE5. baseline and differential.
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.
GeneTreeiENSGT00760000119158.
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

        10         20         30         40         50
MFGDLFEEEY STVSNNQYGK GKKLKTKALE PPAPREFTNL SGIRNQGGTC
60 70 80 90 100
YLNSLLQTLH FTPEFREALF SLGPEELGLF EDKDKPDAKV RIIPLQLQRL
110 120 130 140 150
FAQLLLLDQE AASTADLTDS FGWTSNEEMR QHDVQELNRI LFSALETSLV
160 170 180 190 200
GTSGHDLIYR LYHGTIVNQI VCKECKNVSE RQEDFLDLTV AVKNVSGLED
210 220 230 240 250
ALWNMYVEEE VFDCDNLYHC GTCDRLVKAA KSAKLRKLPP FLTVSLLRFN
260 270 280 290 300
FDFVKCERYK ETSCYTFPLR INLKPFCEQS ELDDLEYIYD LFSVIIHKGG
310 320 330 340 350
CYGGHYHVYI KDVDHLGNWQ FQEEKSKPDV NLKDLQSEEE IDHPLMILKA
360 370 380 390 400
ILLEENNLIP VDQLGQKLLK KIGISWNKKY RKQHGPLRKF LQLHSQIFLL
410 420 430 440 450
SSDESTVRLL KNSSLQAESD FQRNDQQIFK MLPPESPGLN NSISCPHWFD
460 470 480 490 500
INDSKVQPIR EKDIEQQFQG KESAYMLFYR KSQLQRPPEA RANPRYGVPC
510 520 530 540 550
HLLNEMDAAN IELQTKRAEC DSANNTFELH LHLGPQYHFF NGALHPVVSQ
560 570 580 590 600
TESVWDLTFD KRKTLGDLRQ SIFQLLEFWE GDMVLSVAKL VPAGLHIYQS
610 620 630 640 650
LGGDELTLCE TEIADGEDIF VWNGVEVGGV HIQTGIDCEP LLLNVLHLDT
660 670 680 690 700
SSDGEKCCQV IESPHVFPAN AEVGTVLTAL AIPAGVIFIN SAGCPGGEGW
710 720 730 740 750
TAIPKEDMRK TFREQGLRNG SSILIQDSHD DNSLLTKEEK WVTSMNEIDW
760 770 780 790 800
LHVKNLCQLE SEEKQVKISA TVNTMVFDIR IKAIKELKLM KELADNSCLR
810 820 830 840 850
PIDRNGKLLC PVPDSYTLKE AELKMGSSLG LCLGKAPSSS QLFLFFAMGS
860 870 880 890 900
DVQPGTEMEI VVEETISVRD CLKLMLKKSG LQGDAWHLRK MDWCYEAGEP
910 920 930 940 950
LCEEDATLKE LLICSGDTLL LIEGQLPPLG FLKVPIWWYQ LQGPSGHWES
960 970 980 990 1000
HQDQTNCTSS WGRVWRATSS QGASGNEPAQ VSLLYLGDIE ISEDATLAEL
1010 1020 1030 1040 1050
KSQAMTLPPF LEFGVPSPAH LRAWTVERKR PGRLLRTDRQ PLREYKLGRR
1060 1070 1080 1090 1100
IEICLEPLQK GENLGPQDVL LRTQVRIPGE RTYAPALDLV WNAAQGGTAG
1110 1120 1130 1140 1150
SLRQRVADFY RLPVEKIEIA KYFPEKFEWL PISSWNQQIT KRKKKKKQDY
1160 1170 1180 1190 1200
LQGAPYYLKD GDTIGVKNLL IDDDDDFSTI RDDTGKEKQK QRALGRRKSQ
1210 1220 1230
EALHEQSSYI LSSAETPARP RAPETSLSIH VGSFR
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.
GeneTreei ENSGT00760000119158.
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

Bgeei Q9NVE5.
CleanExi HS_USP40.
ExpressionAtlasi Q9NVE5. baseline and differential.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 108 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