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Q8LAM0

- UBP4_ARATH

UniProt

Q8LAM0 - UBP4_ARATH

Protein

Ubiquitin carboxyl-terminal hydrolase 4

Gene

UBP4

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 83 (01 Oct 2014)
      Sequence version 2 (26 Apr 2005)
      Previous versions | rss
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    Functioni

    Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin. Involved in the processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins. Required for the correct development of pollen.2 Publications

    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 sitei32 – 321Nucleophile
    Active sitei310 – 3101Proton 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

    Enzyme and pathway databases

    BioCyciARA:AT2G22310-MONOMER.
    ARA:GQT-1522-MONOMER.

    Protein family/group databases

    MEROPSiC19.092.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 4 (EC:3.4.19.12)
    Alternative name(s):
    Deubiquitinating enzyme 4
    Short name:
    AtUBP4
    Ubiquitin thioesterase 4
    Ubiquitin-specific-processing protease 4
    Gene namesi
    Name:UBP4
    Ordered Locus Names:At2g22310
    ORF Names:T26C19.3
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 2

    Organism-specific databases

    TAIRiAT2G22310.

    Subcellular locationi

    Nucleus 1 Publication

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi32 – 321C → S: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11RemovedSequence Analysis
    Chaini2 – 365364Ubiquitin carboxyl-terminal hydrolase 4PRO_0000080695Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Lipidationi2 – 21N-myristoyl glycine1 Publication

    Keywords - PTMi

    Lipoprotein, Myristate

    Proteomic databases

    PRIDEiQ8LAM0.

    Expressioni

    Tissue specificityi

    Constitutively and ubiquitously expressed.1 Publication

    Gene expression databases

    GenevestigatoriQ8LAM0.

    Structurei

    3D structure databases

    ProteinModelPortaliQ8LAM0.
    SMRiQ8LAM0. Positions 24-339.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini23 – 362340USPAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi81 – 9818Bipartite nuclear localization signalSequence AnalysisAdd
    BLAST

    Sequence similaritiesi

    Belongs to the peptidase C19 family.Curated
    Contains 1 USP domain.Curated

    Phylogenomic databases

    eggNOGiCOG5533.
    HOGENOMiHOG000231498.
    InParanoidiQ8LAM0.
    KOiK11842.
    PhylomeDBiQ8LAM0.

    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]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 1 isoform i produced by alternative splicing. Align

    Note: A number of isoforms are produced. According to EST sequences.

    Isoform 1 (identifier: Q8LAM0-1) [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

    MGAAGSKLEK ALGDQFPEGE RYFGFENFGN TCYCNSVLQA LYFCAPFREQ    50
    LLEHYANNKA DAEENLLTCL ADLFSQISSQ KKKTGVIAPK RFVQRLKKQN 100
    ELFRSYMHQD AHEFLNYLLN ELVEILEKET QATKADNETS SSPEKIANVL 150
    KAPLANGVHK EPIVTWVHKI FQGILTNETR CLRCETVTAR DETFLDLSLD 200
    IEQNSSITSC LKNFSSTETL HAEDKFFCDK CCSLQEAQKR MKIKKPPHIL 250
    VIHLKRFKYM EQLGRYKKLS YRVVFPLELK LSNTVDEYVD IEYSLFAVVV 300
    HVGSGPNHGH YVSLVKSHNH WLFFDDESVE IIEESAVQTF FGSSQEYSSN 350
    TDHGYILLYE SLGTR 365
    Length:365
    Mass (Da):41,846
    Last modified:April 26, 2005 - v2
    Checksum:i23E86CF5FDB0CE6D
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti172 – 1721Q → K in AAM65268. 1 PublicationCurated
    Sequence conflicti334 – 3341E → K in AAM65268. 1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U76846 mRNA. Translation: AAB67967.1.
    AC007168 Genomic DNA. Translation: AAD23612.1.
    CP002685 Genomic DNA. Translation: AEC07291.1.
    AY048261 mRNA. Translation: AAK82523.1.
    AY072625 mRNA. Translation: AAL62016.1.
    AY087731 mRNA. Translation: AAM65268.1.
    PIRiB84611.
    RefSeqiNP_565532.1. NM_127796.3. [Q8LAM0-1]
    UniGeneiAt.48505.
    At.71036.

    Genome annotation databases

    EnsemblPlantsiAT2G22310.1; AT2G22310.1; AT2G22310. [Q8LAM0-1]
    GeneIDi816763.
    KEGGiath:AT2G22310.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U76846 mRNA. Translation: AAB67967.1 .
    AC007168 Genomic DNA. Translation: AAD23612.1 .
    CP002685 Genomic DNA. Translation: AEC07291.1 .
    AY048261 mRNA. Translation: AAK82523.1 .
    AY072625 mRNA. Translation: AAL62016.1 .
    AY087731 mRNA. Translation: AAM65268.1 .
    PIRi B84611.
    RefSeqi NP_565532.1. NM_127796.3. [Q8LAM0-1 ]
    UniGenei At.48505.
    At.71036.

    3D structure databases

    ProteinModelPortali Q8LAM0.
    SMRi Q8LAM0. Positions 24-339.
    ModBasei Search...
    MobiDBi Search...

    Protein family/group databases

    MEROPSi C19.092.

    Proteomic databases

    PRIDEi Q8LAM0.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT2G22310.1 ; AT2G22310.1 ; AT2G22310 . [Q8LAM0-1 ]
    GeneIDi 816763.
    KEGGi ath:AT2G22310.

    Organism-specific databases

    GeneFarmi 4912.
    TAIRi AT2G22310.

    Phylogenomic databases

    eggNOGi COG5533.
    HOGENOMi HOG000231498.
    InParanoidi Q8LAM0.
    KOi K11842.
    PhylomeDBi Q8LAM0.

    Enzyme and pathway databases

    BioCyci ARA:AT2G22310-MONOMER.
    ARA:GQT-1522-MONOMER.

    Gene expression databases

    Genevestigatori Q8LAM0.

    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. "AtUBP3 and AtUBP4 are two closely related Arabidopsis thaliana ubiquitin-specific proteases present in the nucleus."
      Chandler J.S., McArdle B., Callis J.
      Mol. Gen. Genet. 255:302-310(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, MUTAGENESIS OF CYS-32, TISSUE SPECIFICITY.
      Strain: cv. Landsberg erecta.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "Full-length cDNA from Arabidopsis thaliana."
      Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
      Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    6. "Ubiquitin-specific proteases from Arabidopsis thaliana: cloning of AtUBP5 and analysis of substrate specificity of AtUBP3, AtUBP4, and AtUBP5 using Escherichia coli in vivo and in vitro assays."
      Rao-Naik C., Chandler J.S., McArdle B., Callis J.
      Arch. Biochem. Biophys. 379:198-208(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    7. "The ubiquitin-specific protease family from Arabidopsis. AtUBP1 and 2 are required for the resistance to the amino acid analog canavanine."
      Yan N., Doelling J.H., Falbel T.G., Durski A.M., Vierstra R.D.
      Plant Physiol. 124:1828-1843(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE FAMILY ORGANIZATION, NOMENCLATURE.
    8. "Unexpected protein families including cell defense components feature in the N-myristoylome of a higher eukaryote."
      Boisson B., Giglione C., Meinnel T.
      J. Biol. Chem. 278:43418-43429(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: MYRISTOYLATION AT GLY-2.
    9. "The ubiquitin-specific protease subfamily UBP3/UBP4 is essential for pollen development and transmission in Arabidopsis."
      Doelling J.H., Phillips A.R., Soyler-Ogretim G., Wise J., Chandler J.S., Callis J., Otegui M.S., Vierstra R.D.
      Plant Physiol. 145:801-813(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.

    Entry informationi

    Entry nameiUBP4_ARATH
    AccessioniPrimary (citable) accession number: Q8LAM0
    Secondary accession number(s): O24455
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 26, 2005
    Last sequence update: April 26, 2005
    Last modified: October 1, 2014
    This is version 83 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. Peptidase families
      Classification of peptidase families and list of entries
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3