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

Summary

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: mouse all
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
Nuclear RNR-alpha antagonizes cell proliferation by directly inhibiting ZRANB3
Title: Nuclear RNR-α antagonizes cell proliferation by directly inhibiting ZRANB3.
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.
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.
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.
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.
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).
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-85039 (e-PCR)
- UniSTS:103430

D8S2279 (e-PCR)
- UniSTS:473907

RH69631 (e-PCR)
- UniSTS:55629

SHGC-53053 (e-PCR)
- UniSTS:42378

RH48895 (e-PCR)
- UniSTS:41873

WI-20662 (e-PCR)
- UniSTS:43674

RH36331 (e-PCR)
- UniSTS:11200

RH93721 (e-PCR)
- UniSTS:88529

A006P05 (e-PCR)
- UniSTS:82404

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)

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
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
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