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

Gene ID: 121642, updated on 2-Nov-2024

Summary

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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
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Genomic context

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See ALKBH2 in Genome Data Viewer
Location:
12q24.11
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (109088189..109093472, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (109063001..109068284, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (109525994..109531277, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ubiquitin specific peptidase 30 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:109490575-109491074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6983 Neighboring gene USP30 antisense RNA 1 Neighboring gene RNA, 5S ribosomal pseudogene 372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109548634-109549184 Neighboring gene uncharacterized LOC105369974 Neighboring gene uracil DNA glycosylase Neighboring gene acetyl-CoA carboxylase beta

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 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. Individual Contributions of Amido Acid Residues Tyr122, Ile168, and Asp173 to the Activity and Substrate Specificity of Human DNA Dioxygenase ABH2. Davletgildeeva AT, et al. Cells, 2023 Jul 13. PMID 37508504, Free PMC Article
  2. Conformational Dynamics of Human ALKBH2 Dioxygenase in the Course of DNA Repair as Revealed by Stopped-Flow Fluorescence Spectroscopy. Kanazhevskaya LY, et al. Molecules, 2022 Aug 4. PMID 35956910, Free PMC Article
  3. Frequent down-regulation of hABH2 in gastric cancer and its involvement in growth of cancer cells. Gao W, et al. J Gastroenterol Hepatol, 2011 Mar. PMID 21155885
  4. X-ray absorption spectroscopy structural investigation of early intermediates in the mechanism of DNA repair by human ABH2. Giri NC, et al. Biochemistry, 2011 Jun 7. PMID 21510633, Free PMC Article
  5. TP53 regulates human AlkB homologue 2 expression in glioma resistance to Photofrin-mediated photodynamic therapy. Lee SY, et al. Br J Cancer, 2010 Jul 27. PMID 20661249, Free PMC Article

See all (49) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ99103, MGC90512

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
NP_001138846.1
NP_001138847.1
NP_001192108.1
NP_001192109.1
XP_005253892.1
XP_005253893.1
XP_047284265.1
XP_054227093.1
XP_054227094.1
XP_054227095.1

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_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

  2. 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

  3. 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

  4. 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

  5. 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_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    109088189..109093472 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Related
    ENSP00000399820.2, ENST00000440112.2

  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

  3. 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

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    109063001..109068284 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371120.1 → XP_054227095.1  DNA oxidative demethylase ALKBH2 isoform X2

  2. XM_054371118.1 → XP_054227093.1  DNA oxidative demethylase ALKBH2 isoform X1

    UniProtKB/Swiss-Prot
    A4PET2, Q5XLE3, Q6NS38

  3. XM_054371119.1 → XP_054227094.1  DNA oxidative demethylase ALKBH2 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6NS38.1 GenPept UniProtKB/Swiss-Prot:Q6NS38

Gene LinkOut

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