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ZRANB3 zinc finger RANBP2-type containing 3 [ Homo sapiens (human) ]

Gene ID: 84083, updated on 5-Mar-2024

Summary

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Official Symbol
ZRANB3provided by HGNC
Official Full Name
zinc finger RANBP2-type containing 3provided by HGNC
Primary source
HGNC:HGNC:25249
See related
Ensembl:ENSG00000121988 MIM:615655; AllianceGenome:HGNC:25249
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AH2; 4933425L19Rik
Summary
Enables ATP-dependent DNA/DNA annealing activity; K63-linked polyubiquitin modification-dependent protein binding activity; and endodeoxyribonuclease activity. Involved in several processes, including DNA metabolic process; DNA rewinding; and negative regulation of DNA recombination. Located in nuclear replication fork and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 1.8), thyroid (RPKM 0.8) and 24 other tissues See more
Orthologs
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Genomic context

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See ZRANB3 in Genome Data Viewer
Location:
2q21.3
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (135196969..135531218, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (135637447..135971741, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (135954539..136288788, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene RAB3 GTPase activating protein catalytic subunit 1 Neighboring gene HNF4 motif-containing MPRA enhancer 203 Neighboring gene small nucleolar RNA, H/ACA box 40B Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:135970274-135970798 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:135980911-135981075 Neighboring gene uncharacterized LOC124906077 Neighboring gene MPRA-validated peak3875 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16571 Neighboring gene Sharpr-MPRA regulatory region 5980 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16572 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11981 Neighboring gene G3BP1 pseudogene 1 Neighboring gene R3H domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16574 Neighboring gene uncharacterized LOC124907893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16575 Neighboring gene RNA, U6 small nuclear 512, pseudogene Neighboring gene microRNA 128-1

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. Structural insights into the function of ZRANB3 in replication stress response. Sebesta M, et al. Nat Commun, 2017 Jun 16. PMID 28621305, Free PMC Article
  2. Identification of a Substrate Recognition Domain in the Replication Stress Response Protein Zinc Finger Ran-binding Domain-containing Protein 3 (ZRANB3). Badu-Nkansah A, et al. J Biol Chem, 2016 Apr 8. PMID 26884333, Free PMC Article
  3. RFWD3 promotes ZRANB3 recruitment to regulate the remodeling of stalled replication forks. Moore CE, et al. J Cell Biol, 2023 May 1. PMID 37036693, Free PMC Article
  4. Nuclear RNR-α antagonizes cell proliferation by directly inhibiting ZRANB3. Fu Y, et al. Nat Chem Biol, 2018 Oct. PMID 30150681, Free PMC Article
  5. Replication Fork Slowing and Reversal upon DNA Damage Require PCNA Polyubiquitination and ZRANB3 DNA Translocase Activity. Vujanovic M, et al. Mol Cell, 2017 Sep 7. PMID 28886337, Free PMC Article

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RFWD3 promotes ZRANB3 recruitment to regulate the remodeling of stalled replication forks.
    Title: RFWD3 promotes ZRANB3 recruitment to regulate the remodeling of stalled replication forks.
  2. Time for remodeling: SNF2-family DNA translocases in replication fork metabolism and human disease.
    Title: Time for remodeling: SNF2-family DNA translocases in replication fork metabolism and human disease.
  3. ZRANB3 is an African-specific type 2 diabetes locus associated with beta-cell mass and insulin response.
    Title: ZRANB3 is an African-specific type 2 diabetes locus associated with beta-cell mass and insulin response.
  4. Nuclear RNR-alpha antagonizes cell proliferation by directly inhibiting ZRANB3
    Title: Nuclear RNR-α antagonizes cell proliferation by directly inhibiting ZRANB3.
  5. PCNA and ATP-dependency serve as a multi-layered regulatory mechanism that modulates ZRANB3 activity at replication forks.
    Title: Structural insights into the function of ZRANB3 in replication stress response.
  6. A large number of SNF2 family, DNA and ATP-dependent motor proteins are needed during transcription, DNA replication, and DNA repair to manipulate protein-DNA interactions and change DNA structure. SMARCAL1, ZRANB3, and HLTF are three related members of this family with specialized functions that maintain genome stability during DNA replication. [review]
    Title: Functions of SMARCAL1, ZRANB3, and HLTF in maintaining genome stability.
  7. depletion of SMARCAL1, a SNF2-family DNA translocase that remodels stalled forks, restores replication fork stability and reduces the formation of replication stress-induced DNA breaks and chromosomal aberrations in BRCA1/2-deficient cells. In addition to SMARCAL1, other SNF2-family fork remodelers, including ZRANB3 and HLTF, cause nascent DNA degradation and genomic instability
    Title: Restoration of Replication Fork Stability in BRCA1- and BRCA2-Deficient Cells by Inactivation of SNF2-Family Fork Remodelers.
  8. Damage-induced fork reversal in mammalian cells requires PCNA ubiquitination, UBC13, and K63-linked polyubiquitin chains, previously involved in error-free damage tolerance. Fork reversal in vivo also requires ZRANB3 translocase activity and its interaction with polyubiquitinated PCNA, pinpointing ZRANB3 as a key effector of error-free DNA damage tolerance.
    Title: Replication Fork Slowing and Reversal upon DNA Damage Require PCNA Polyubiquitination and ZRANB3 DNA Translocase Activity.
  9. Here is described a substrate recognition domain within ZRANB3 that is needed for it to recognize forked DNA structures, hydrolyze ATP, catalyze fork remodeling, and act as a structure-specific endonuclease.
    Title: Identification of a Substrate Recognition Domain in the Replication Stress Response Protein Zinc Finger Ran-binding Domain-containing Protein 3 (ZRANB3).
  10. AH2 is recruited to stalled replication forks and that cells depleted of AH2 are hypersensitive to replication stresses.
    Title: The HARP-like domain-containing protein AH2/ZRANB3 binds to PCNA and participates in cellular response to replication stress.
Submit: New GeneRIF Correction See all GeneRIFs (14)

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC75012, MGC105033

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP-dependent DNA/DNA annealing activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ATP-dependent chromatin remodeler activity IEA
Inferred from Electronic Annotation
more info
  
enables DNA endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
NOT enables DNA helicase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables K63-linked polyubiquitin modification-dependent protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in DNA repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA rewinding IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA recombination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in replication fork processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in replication fork processing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in replication fork reversal IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to UV IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in nuclear replication fork IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nuclear replication fork IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
DNA annealing helicase and endonuclease ZRANB3
Names
annealing helicase 2
zinc finger Ran-binding domain-containing protein 3
zinc finger, RAN-binding domain containing 3

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_001286568.2 → NP_001273497.1  DNA annealing helicase and endonuclease ZRANB3 isoform 2

    See identical proteins and their annotated locations for NP_001273497.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and uses an alternate splice site in the central coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC017031, AI670931, BX647838
    Consensus CDS
    CCDS67963.1
    UniProtKB/Swiss-Prot
    Q5FWF4
    Related
    ENSP00000383979.1, ENST00000401392.5
    Conserved Domains (6) summary
    cd00046
    Location:55 → 190
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00085
    Location:1009 → 1047
    HNHc; HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and ...
    sd00029
    Location:625 → 644
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam00176
    Location:40 → 316
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:330 → 435
    Helicase_C; Helicase conserved C-terminal domain
    pfam00641
    Location:625 → 647
    zf-RanBP; Zn-finger in Ran binding protein and others

  2. NM_001286569.1 → NP_001273498.1  DNA annealing helicase and endonuclease ZRANB3 isoform 3

    See identical proteins and their annotated locations for NP_001273498.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR which results in the use of a downstream start codon compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AC016742, AC017031, AC064850, AI670931, AL833322
    Consensus CDS
    CCDS74580.1
    UniProtKB/TrEMBL
    F5GYN7
    Related
    ENSP00000441320.2, ENST00000536680.5
    Conserved Domains (3) summary
    cd00085
    Location:557 → 595
    HNHc; HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and ...
    sd00029
    Location:171 → 190
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam00641
    Location:171 → 193
    zf-RanBP; Zn-finger in Ran binding protein and others

  3. NM_032143.4 → NP_115519.2  DNA annealing helicase and endonuclease ZRANB3 isoform 1

    See identical proteins and their annotated locations for NP_115519.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform 1.
    Source sequence(s)
    AC017031, AI670931, BC089429
    Consensus CDS
    CCDS46419.1
    UniProtKB/Swiss-Prot
    B3KYA1, B4E375, B5MDI3, D3DP76, E9PBP0, Q53SM1, Q5FWF4, Q6P2C4, Q8N1P4, Q9H0E8
    Related
    ENSP00000264159.6, ENST00000264159.11
    Conserved Domains (6) summary
    cd00046
    Location:55 → 190
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00085
    Location:1011 → 1049
    HNHc; HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and ...
    sd00029
    Location:625 → 644
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam00176
    Location:40 → 316
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:330 → 435
    Helicase_C; Helicase conserved C-terminal domain
    pfam00641
    Location:625 → 647
    zf-RanBP; Zn-finger in Ran binding protein and others

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    135196969..135531218 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    135637447..135971741 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5FWF4.2 GenPept UniProtKB/Swiss-Prot:Q5FWF4

Gene LinkOut

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