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    ZUP1 zinc finger containing ubiquitin peptidase 1 [ Homo sapiens (human) ]

    Gene ID: 221302, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ZUP1provided by HGNC
    Official Full Name
    zinc finger containing ubiquitin peptidase 1provided by HGNC
    Primary source
    HGNC:HGNC:21224
    See related
    Ensembl:ENSG00000153975 MIM:620543; AllianceGenome:HGNC:21224
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DUB; ZUFSP; C6orf113
    Summary
    This gene encodes a protein containing zinc finger motifs and a cysteine peptidase domain. The encoded protein functions as a K63-specific de-ubiquitinating enzyme that specifically cleaves long K63-linked polyubiquitin chains in the middle of a chain (i.e. "endo cleavage) rather than by removing the terminal ubiquitin from a chain. This enzyme is thought to be involved in the regulation of DNA repair by cleaving K63-linked ubiquitin chains at repair foci. This protein is related to proteases for the ubiquitin-like modifiers Ufm1 (ubiquitin fold modifier 1) and Atg8/Gabarapl2, but does not have any activity on these modifiers. [provided by RefSeq, Mar 2018]
    Expression
    Ubiquitous expression in duodenum (RPKM 4.7), bone marrow (RPKM 4.6) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See ZUP1 in Genome Data Viewer
    Location:
    6q22.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (116635618..116668766, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (117819329..117852469, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (116956781..116989929, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17496 Neighboring gene RWD domain containing 1 Neighboring gene MPRA-validated peak6052 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24997 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24998 Neighboring gene uncharacterized LOC124901386 Neighboring gene radial spoke head component 4A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17497 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24999 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:117001971-117002954 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:117002955-117003936 Neighboring gene karyopherin subunit alpha 5 Neighboring gene uncharacterized LOC124901560 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:117085903-117086417 Neighboring gene family with sequence similarity 162 member B

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Functional Analysis of Single Nucleotide Polymorphism in ZUFSP Protein and Implication in Pathogenesis. Ajadi MB, et al. Protein J, 2021 Feb. PMID 33512633
    2. ZUFSP Deubiquitylates K63-Linked Polyubiquitin Chains to Promote Genome Stability. Haahr P, et al. Mol Cell, 2018 Apr 5. PMID 29576528
    3. A family of unconventional deubiquitinases with modular chain specificity determinants. Hermanns T, et al. Nat Commun, 2018 Feb 23. PMID 29476094, Free PMC Article
    4. Identifying protein partners of CLN8, an ER-resident protein involved in neuronal ceroid lipofuscinosis. Passantino R, et al. Biochim Biophys Acta, 2013 Mar. PMID 23142642
    5. Reactive-site-centric chemoproteomics identifies a distinct class of deubiquitinase enzymes. Hewings DS, et al. Nat Commun, 2018 Mar 21. PMID 29563501, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Functional Analysis of Single Nucleotide Polymorphism in ZUFSP Protein and Implication in Pathogenesis.
      Title: Functional Analysis of Single Nucleotide Polymorphism in ZUFSP Protein and Implication in Pathogenesis.
    2. ZUFSP is recruited to and regulates K63-Ub conjugates at genotoxic stress sites, promoting chromosome stability upon replication stress in a manner dependent on its catalytic activity.
      Title: ZUFSP Deubiquitylates K63-Linked Polyubiquitin Chains to Promote Genome Stability.
    3. Identify two ubiquitin binding domains in ZUFSP: a ZHA (ZUFSP helical arm) that binds to the distal ubiquitin and an atypical UBZ domain in ZUFSP that binds to polyubiquitin. Importantly, both domains are essential for ZUFSP to selectively cleave K63-linked polyubiquitin.
      Title: Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability.
    4. ZUFSP,the singular human member of this family, which contains multiple ubiquitin-binding domains responsible for the specific action on K63-linked chains.
      Title: A family of unconventional deubiquitinases with modular chain specificity determinants.
    5. ZUFSP (ZUP1) is a K63-specific deubiquitinating enzyme that is distantly related to proteases for the ubiquitin-like modifiers Ufm1 and Atg8. ZUFSP does not have any activity on these modifiers. ZUFSP specifically cleaves long K63-linked poly-ubiquitin chains in an ""endo"" mode, i.e. cleavage takes place in the middle of a chain rather than by removing the terminal ubiquitin from a chain.
      Title: A family of unconventional deubiquitinases with modular chain specificity determinants.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of zinc finger with UFM1-specific peptidase domain (ZUFSP) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cysteine-type deubiquitinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger-containing ubiquitin peptidase 1
    Names
    lys-63-specific deubiquitinase ZUFSP
    ubiquitin carboxyl-terminal hydrolase ZUFSP
    zinc finger with UFM1-specific peptidase domain protein
    NP_001348118.1
    NP_001348119.1
    NP_001348120.1
    NP_659499.2

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001361189.2 → NP_001348118.1  zinc finger-containing ubiquitin peptidase 1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL132795
      Consensus CDS
      CCDS5110.1
      UniProtKB/Swiss-Prot
      Q5TD92, Q6PJH7, Q96AP4, Q96NV6
      UniProtKB/TrEMBL
      A0A0S2Z605, A0A0S2Z644
      Conserved Domains (1) summary
      pfam07910
      Location:336 → 551
      Peptidase_C78; Peptidase family C78

    2. NM_001361190.2 → NP_001348119.1  zinc finger-containing ubiquitin peptidase 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL132795
      Conserved Domains (1) summary
      pfam07910
      Location:168 → 383
      Peptidase_C78; Peptidase family C78

    3. NM_001361191.2 → NP_001348120.1  zinc finger-containing ubiquitin peptidase 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL132795
      Conserved Domains (1) summary
      pfam07910
      Location:140 → 355
      Peptidase_C78; Peptidase family C78

    4. NM_145062.3 → NP_659499.2  zinc finger-containing ubiquitin peptidase 1 isoform 1

      See identical proteins and their annotated locations for NP_659499.2

      Status: REVIEWED

      Source sequence(s)
      BC016879
      Consensus CDS
      CCDS5110.1
      UniProtKB/Swiss-Prot
      Q5TD92, Q6PJH7, Q96AP4, Q96NV6
      UniProtKB/TrEMBL
      A0A0S2Z605, A0A0S2Z644
      Related
      ENSP00000357565.3, ENST00000368576.8
      Conserved Domains (1) summary
      pfam07910
      Location:336 → 551
      Peptidase_C78; Peptidase family C78

    RNA

    1. NR_154586.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL132795

    2. NR_154587.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL132795

    3. NR_154588.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL132795

    4. NR_154589.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL132795

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      116635618..116668766 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      117819329..117852469 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96AP4.1 GenPept UniProtKB/Swiss-Prot:Q96AP4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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