ALKBH2 alkB homolog 2, alpha-ketoglutarate dependent dioxygenase [Homo sapiens (human)] - Gene

Summary

Official Symbol: ALKBH2provided by HGNC
Official Full Name: alkB homolog 2, alpha-ketoglutarate dependent dioxygenaseprovided by HGNC
Primary source: HGNC:HGNC:32487
See related: Ensembl:ENSG00000189046 MIM:610602; AllianceGenome:HGNC:32487
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: ABH2
Summary: The Escherichia coli AlkB protein protects against the cytotoxicity of methylating agents by repair of the specific DNA lesions generated in single-stranded DNA. ALKBH2 and ALKBH3 (MIM 610603) are E. coli AlkB homologs that catalyze the removal of 1-methyladenine and 3-methylcytosine (Duncan et al., 2002 [PubMed 12486230]).[supplied by OMIM, Mar 2008]
Expression: Ubiquitous expression in ovary (RPKM 6.9), endometrium (RPKM 5.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q24.11

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (109088189..109093472, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (109063001..109068284, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (109525994..109531277, complement)

Chromosome 12 - NC_000012.12 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?

Individual Contributions of Amido Acid Residues Tyr122, Ile168, and Asp173 to the Activity and Substrate Specificity of Human DNA Dioxygenase ABH2.
Title: Individual Contributions of Amido Acid Residues Tyr122, Ile168, and Asp173 to the Activity and Substrate Specificity of Human DNA Dioxygenase ABH2.
Conformational Dynamics of Human ALKBH2 Dioxygenase in the Course of DNA Repair as Revealed by Stopped-Flow Fluorescence Spectroscopy.
Title: Conformational Dynamics of Human ALKBH2 Dioxygenase in the Course of DNA Repair as Revealed by Stopped-Flow Fluorescence Spectroscopy.
ALKBH2 inhibition alleviates malignancy in colorectal cancer by regulating BMI1-mediated activation of NF-kappaB pathway.
Title: ALKBH2 inhibition alleviates malignancy in colorectal cancer by regulating BMI1-mediated activation of NF-κB pathway.
Insights into the Direct Oxidative Repair of Etheno Lesions: MD and QM/MM Study on the Substrate Scope of ALKBH2 and AlkB.
Title: Insights into the Direct Oxidative Repair of Etheno Lesions: MD and QM/MM Study on the Substrate Scope of ALKBH2 and AlkB.
Data show that the three DNA repair enzymes ALKBH2, ALKBH3, and AlkB are not only able to repair DNA adducts, but also can edit the epigenetic modification and generate the corresponding oxidative derivatives.
Title: DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro.
These results revealed that N3-ethylthymidine , but not other DNA lesions, could be repaired by Alkbh2 and Alkbh3 in mammalian cells.
Title: Roles of Aag, Alkbh2, and Alkbh3 in the Repair of Carboxymethylated and Ethylated Thymidine Lesions.
studies reveal the ALKBH2 binding interface of PCNA and indicate that both germline and somatic ALKBH2 variants could have cellular effects on ALKBH2 function in DNA repair.
Title: The interaction between ALKBH2 DNA repair enzyme and PCNA is direct, mediated by the hydrophobic pocket of PCNA and perturbed in naturally-occurring ALKBH2 variants.
It was shown for first time that DNA glycosylase ALKBH2 can repair DNA adduct 1,N2-ethenoguanine.
Title: Differential repair of etheno-DNA adducts by bacterial and human AlkB proteins.
ABH2 knockdown impairs rDNA transcription and leads to increased single-stranded and double-stranded DNA breaks in the rDNA genes.
Title: ABH2 couples regulation of ribosomal DNA transcription with DNA alkylation repair.
Overexpression of ALKBH2 is associated with enhanced resistance to temozolomide in glioblastoma.
Title: The DNA repair protein ALKBH2 mediates temozolomide resistance in human glioblastoma cells.

Submit: New GeneRIF Correction See all GeneRIFs (23)

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

WI-20815 (e-PCR)
- UniSTS:1668

D20S1119 (e-PCR)
- UniSTS:40845

RH45951 (e-PCR)
- UniSTS:11230

STS-D60111 (e-PCR)
- UniSTS:57312

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables broad specificity oxidative DNA demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables broad specificity oxidative DNA demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables cytosine C-5 DNA demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables cytosine C-5 DNA demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables ferrous iron binding	IBA Inferred from Biological aspect of Ancestor more info
enables ferrous iron binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables rDNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA alkylation repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA alkylation repair	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: DNA oxidative demethylase ALKBH2

Names: 2OG-Fe(II) oxy DC1; alkB, alkylation repair homolog 2; alkylated DNA repair protein alkB homolog 2; alpha-ketoglutarate-dependent dioxygenase alkB homolog 2; oxy DC1

NP_001001655.1

EC 1.14.11.33

NP_001138846.1

EC 1.14.11.33

NP_001138847.1

EC 1.14.11.33

NP_001192108.1

EC 1.14.11.33

NP_001192109.1

EC 1.14.11.33

XP_005253892.1

EC 1.14.11.33

XP_005253893.1

EC 1.14.11.33

XP_047284265.1

EC 1.14.11.33

XP_054227093.1

EC 1.14.11.33

XP_054227094.1

EC 1.14.11.33

XP_054227095.1

EC 1.14.11.33

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_001001655.3 → NP_001001655.1 DNA oxidative demethylase ALKBH2 isoform 1

See identical proteins and their annotated locations for NP_001001655.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1-3 encode the same protein.

Source sequence(s)

AI278638, BC070489, BM785502

Consensus CDS

CCDS31897.1

UniProtKB/Swiss-Prot

A4PET2, Q5XLE3, Q6NS38

Related

ENSP00000343021.3, ENST00000343075.7

Conserved Domains (1) summary

pfam13532
Location:72 → 254

2OG-FeII_Oxy_2; 2OG-Fe(II) oxygenase superfamily
NM_001145374.2 → NP_001138846.1 DNA oxidative demethylase ALKBH2 isoform 1

See identical proteins and their annotated locations for NP_001138846.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1-3 encode the same protein.

Source sequence(s)

AC011596, AI278638, BM820131, DA182735

Consensus CDS

CCDS31897.1

UniProtKB/Swiss-Prot

A4PET2, Q5XLE3, Q6NS38

Related

ENSP00000398181.1, ENST00000429722.3

Conserved Domains (1) summary

pfam13532
Location:72 → 254

2OG-FeII_Oxy_2; 2OG-Fe(II) oxygenase superfamily
NM_001145375.2 → NP_001138847.1 DNA oxidative demethylase ALKBH2 isoform 1

See identical proteins and their annotated locations for NP_001138847.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-3 encode the same protein.

Source sequence(s)

AC011596, AI278638, BM785502, BM790974

Consensus CDS

CCDS31897.1

UniProtKB/Swiss-Prot

A4PET2, Q5XLE3, Q6NS38

Conserved Domains (1) summary

pfam13532
Location:72 → 254

2OG-FeII_Oxy_2; 2OG-Fe(II) oxygenase superfamily
NM_001205179.2 → NP_001192108.1 DNA oxidative demethylase ALKBH2 isoform 2

See identical proteins and their annotated locations for NP_001192108.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and lacks a coding exon compared to variant 1. The resulting protein (isoform 2) is shorter but has the same N- and C-termini compared to isoform 1. Variants 4 and 5 encode the same protein.

Source sequence(s)

AB277859, AC011596, AI278638, CN421655

Consensus CDS

CCDS55883.1

UniProtKB/Swiss-Prot

Q6NS38

Related

ENSP00000478765.1, ENST00000619381.4
NM_001205180.2 → NP_001192109.1 DNA oxidative demethylase ALKBH2 isoform 2

See identical proteins and their annotated locations for NP_001192109.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks a coding exon compared to variant 1. The resulting protein (isoform 2) is shorter but has the same N- and C-termini compared to isoform 1. Variants 4 and 5 encode the same protein.

Source sequence(s)

AB277859, AI278638, BM785502

Consensus CDS

CCDS55883.1

UniProtKB/Swiss-Prot

Q6NS38

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

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

109088189..109093472 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047428309.1 → XP_047284265.1 DNA oxidative demethylase ALKBH2 isoform X2

Related

ENSP00000399820.2, ENST00000440112.2
XM_005253835.6 → XP_005253892.1 DNA oxidative demethylase ALKBH2 isoform X1

See identical proteins and their annotated locations for XP_005253892.1

UniProtKB/Swiss-Prot

A4PET2, Q5XLE3, Q6NS38

Conserved Domains (1) summary

pfam13532
Location:72 → 254

2OG-FeII_Oxy_2; 2OG-Fe(II) oxygenase superfamily
XM_005253836.2 → XP_005253893.1 DNA oxidative demethylase ALKBH2 isoform X2

See identical proteins and their annotated locations for XP_005253893.1

UniProtKB/Swiss-Prot

Q6NS38

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

109063001..109068284 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054371120.1 → XP_054227095.1 DNA oxidative demethylase ALKBH2 isoform X2
XM_054371118.1 → XP_054227093.1 DNA oxidative demethylase ALKBH2 isoform X1

UniProtKB/Swiss-Prot

A4PET2, Q5XLE3, Q6NS38
XM_054371119.1 → XP_054227094.1 DNA oxidative demethylase ALKBH2 isoform X2