APOBEC3B apolipoprotein B mRNA editing enzyme catalytic subunit 3B [Homo sapiens (human)] - Gene

Summary

Official Symbol: APOBEC3Bprovided by HGNC
Official Full Name: apolipoprotein B mRNA editing enzyme catalytic subunit 3Bprovided by HGNC
Primary source: HGNC:HGNC:17352
See related: Ensembl:ENSG00000179750 MIM:607110; Vega:OTTHUMG00000151085
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: A3B; ARP4; ARCD3; PHRBNL; APOBEC1L; bK150C2.2; DJ742C19.2
Summary: This gene is a member of the cytidine deaminase gene family. It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1. It is thought that the proteins may be RNA editing enzymes and have roles in growth or cell cycle control. A hybrid gene results from the deletion of approximately 29.5 kb of sequence between this gene, APOBEC3B, and the adjacent gene APOBEC3A. The breakpoints of the deletion are within the two genes, so the deletion allele is predicted to have the promoter and coding region of APOBEC3A, but the 3' UTR of APOBEC3B. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012]
Expression: Biased expression in bone marrow (RPKM 23.5), appendix (RPKM 8.8) and 12 other tissues See more
Orthologs: all

Genomic context

Location:: 22q13.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
109	current	GRCh38.p12 (GCF_000001405.38)	22	NC_000022.11 (38982399..38992779)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (39378352..39388784)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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 Jun 15 11:32:44 2016

Bibliography

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GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

These studies combine to indicate that APOBEC3B promotes drug resistance in breast cancer and that inhibiting APOBEC3B-dependent tumor evolvability may be an effective strategy to improve efficacies of targeted cancer therapies.
Title: The DNA cytosine deaminase APOBEC3B promotes tamoxifen resistance in ER-positive breast cancer.
Our results provide evidence that APOBEC3B can interact with HBV core protein and edit HBV DNAs during reverse transcription. These data suggest that APOBEC3B exerts multifaceted antiviral effects against HBV.
Title: APOBEC3B edits HBV DNA and inhibits HBV replication during reverse transcription.
review of current understanding of APOBEC3A and APOBEC3B biology in human papillomavirus Infection restriction, evolution, and associated cancer mutagenesis
Title: Roles of APOBEC3A and APOBEC3B in Human Papillomavirus Infection and Disease Progression.
This study found that A3B C-terminal domain shows higher activity toward its target sequence in short ssDNA and efficiently deaminates a target sequence located near the center of ssDNA.
Title: Observation by Real-Time NMR and Interpretation of Length- and Location-Dependent Deamination Activity of APOBEC3B.
Data show that the larger oligomeric state of APOBEC3B (A3B) inhibited its activity.
Title: Enzyme cycling contributes to efficient induction of genome mutagenesis by the cytidine deaminase APOBEC3B.
APOBEC3B*c.783delG showed evidence of modest association with breast cancer and seemed to contribute to earlier onset of the disease.
Title: Assessment of an APOBEC3B truncating mutation, c.783delG, in patients with breast cancer.
Data show that APOBEC3B (A3B) expression is inversely related to p53 status in different cancer types and demonstrate that this is due to a direct and pivotal role for p53 in repressing A3B expression.
Title: p53 controls expression of the DNA deaminase APOBEC3B to limit its potential mutagenic activity in cancer cells.
Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation have been reported.
Title: Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation.
A lysine-free derivative of human APOBEC3B was constructed and shown to be indistinguishable from the wild-type enzyme in DNA cytosine deamination, HIV-1 restriction, and nuclear localization activities.
Title: APOBEC3B lysine residues are dispensable for DNA cytosine deamination, HIV-1 restriction, and nuclear localization.
exposures to relevant environmental factors might induce APOBEC3A or APOBEC3B expression above genotoxic levels and initiate tumorigenesis in a tissue-specific manner in the right cellular environment where ssDNA is available
Title: Association of germline variants in the APOBEC3 region with cancer risk and enrichment with APOBEC-signature mutations in tumors.

Submit: New GeneRIF Correction See all GeneRIFs (85)

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

NHGRI GWAS Catalog

Description
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases. NHGRI GWA Catalog NHGRI GWA CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
HIV-1 replication is inhibited by APOBEC3B and APOBEC3G in 293T cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	APOBEC3B may be incorporated into virions by HIV-1 Gag polyprotein	PubMed
Vif	vif	HIV-1 Vif(HXB2) degrades APOBEC3B, and the Vif(HXB2) mutants E128K and F296K have a reduced ability to degrade APOBEC3B in cells	PubMed
	vif	Both HIV-1 Vif(IIIB) and Vif(HXB2) induce polyubiquitination of APOBEC3B at position K63, but only Vif(HXB2) induces polyubiquitination of APOBEC3B at position K48	PubMed
	vif	Human APOBEC3B is able to inhibit HIV infectivity even in the presence of HIV-1 Vif by the G to A hypermutation	PubMed
	vif	Vif(IIIB) induces A3A, A3B, and A3C emigration from the nucleus to the cytosol and thereby causes net increases in their cytosolic concentrations and anti-HIV-1 activities	PubMed
	vif	Stress causes A3A, A3B, A3C, and A3F to co-localize efficiently with Vif(IIIB) and mRNA-PABP1 complexes in stress granules	PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

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Formation of the Editosome, organism-specific biosystem (from REACTOME)
Formation of the Editosome, organism-specific biosystemThe editosome for C to U editing in mammals consist of a member of cytidine deaminase family of enzymes, apoB mRNA editig catalytic polypeptide 1 (APOBEC-1) and a complementing specificity factor (AC...
Gene Expression, organism-specific biosystem (from REACTOME)
Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
mRNA Editing, organism-specific biosystem (from REACTOME)
mRNA Editing, organism-specific biosystemAfter transcription, some RNA molecules are altered to contain bases not encoded in the genome. Most often this involves the editing or modification of one base to another, but in some organisms can ...
mRNA Editing: C to U Conversion, organism-specific biosystem (from REACTOME)
mRNA Editing: C to U Conversion, organism-specific biosystemThe best characterized case of C to U editing is in the intestinal apolipoprotein B transcript, where the editing event creates a premature translation stop codon and consequently leads to a shorter ...

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Homologs of the APOBEC3B gene: The APOBEC3B gene is conserved in chimpanzee, dog, cow, mouse, and rat.
Orthologs from Annotation Pipeline: 16 organisms have orthologs with human gene APOBEC3B
The Hierarchical Catalog of Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
RNA binding	HDA more info	PubMed
RNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
cytidine deaminase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
deoxycytidine deaminase activity	IMP Inferred from Mutant Phenotype more info	PubMed
zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
DNA demethylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
cytidine deamination	IEA Inferred from Electronic Annotation more info
cytidine to uridine editing	IBA Inferred from Biological aspect of Ancestor more info	PubMed
defense response to virus	IDA Inferred from Direct Assay more info	PubMed
innate immune response	IEA Inferred from Electronic Annotation more info
negative regulation of transposition	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
cytoplasm	IBA Inferred from Biological aspect of Ancestor more info	PubMed
nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: DNA dC->dU-editing enzyme APOBEC-3B

Names: apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B; cytidine deaminase; phorbolin 2; phorbolin 3; phorbolin-1-related protein; phorbolin-2/3; probable DNA dC->dU-editing enzyme APOBEC-3B

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_001270411.1 → NP_001257340.1 DNA dC->dU-editing enzyme APOBEC-3B isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site at the 5' end of a coding exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AK024854, AU098564, AY743217, BX114955, CT841510, U61083

Consensus CDS

CCDS58807.1

UniProtKB/Swiss-Prot

Q9UH17

Related

ENSP00000385068.3, OTTHUMP00000199090, ENST00000407298.7, OTTHUMT00000321235

Conserved Domains (3) summary

cd01283
Location:8 → 158

cytidine_deaminase; Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on ...

pfam05240
Location:129 → 174

APOBEC_C; APOBEC-like C-terminal domain

pfam08210
Location:17 → 187

APOBEC_N; APOBEC-like N-terminal domain
NM_004900.4 → NP_004891.4 DNA dC->dU-editing enzyme APOBEC-3B isoform a

See identical proteins and their annotated locations for NP_004891.4

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AL022318, AU098564, AY743217, BX114955, U61083

Consensus CDS

CCDS13982.1

UniProtKB/Swiss-Prot

Q9UH17

Related

ENSP00000327459.3, OTTHUMP00000199088, ENST00000333467.3, OTTHUMT00000321233

Conserved Domains (3) summary

cd01283
Location:8 → 158

cytidine_deaminase; Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on ...

pfam05240
Location:129 → 174

APOBEC_C; APOBEC-like C-terminal domain

pfam08210
Location:17 → 187

APOBEC_N; APOBEC-like N-terminal domain