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

Gene ID: 221302, updated on 5-Mar-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (116635618..116668766, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (117819329..117852469, complement)
105.20220307 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
  • 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 (22) 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_2023_10

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

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