Rhea - reaction knowledgebase

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Name^help_outline an N⁶-methyl-2'-deoxyadenosine in DNA Identifier RHEA-COMP:12419 Reactive part ^help_outline
- Name ^help_outline N⁶-methyl-dAMP residue Identifier CHEBI:90616 Charge -1 Formula C11H13N5O5P SMILES^help_outline N(C1=NC=NC2=C1N=CN2[C@@H]3O[C@H](COP(=O)(*)[O-])[C@@H](O*)C3)C 2D coordinates Mol file for the small molecule Search links Involved in 2 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Search links Involved in 2 reaction(s) Find proteins in UniProtKB for this molecule
Name ^help_outline 2-oxoglutarate Identifier CHEBI:16810 (CAS: 64-15-3) ^help_outline Charge -2 Formula C5H4O5 InChIKey^help_outline KPGXRSRHYNQIFN-UHFFFAOYSA-L SMILES^help_outline [O-]C(=O)CCC(=O)C([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 440 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline O₂ Identifier CHEBI:15379 (CAS: 7782-44-7) ^help_outline Charge 0 Formula O2 InChIKey^help_outline MYMOFIZGZYHOMD-UHFFFAOYSA-N SMILES^help_outline O=O 2D coordinates Mol file for the small molecule Search links Involved in 2,779 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name^help_outline a 2'-deoxyadenosine in DNA Identifier RHEA-COMP:12418 Reactive part ^help_outline
- Name ^help_outline dAMP residue Identifier CHEBI:90615 Charge -1 Formula C10H11N5O5P SMILES^help_outline NC1=NC=NC2=C1N=CN2[C@@H]3O[C@H](COP(=O)(*)[O-])[C@@H](O*)C3 2D coordinates Mol file for the small molecule Search links Involved in 8 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Search links Involved in 3 reaction(s) Find proteins in UniProtKB for this molecule
Name ^help_outline formaldehyde Identifier CHEBI:16842 (CAS: 50-00-0) ^help_outline Charge 0 Formula CH2O InChIKey^help_outline WSFSSNUMVMOOMR-UHFFFAOYSA-N SMILES^help_outline [H]C([H])=O 2D coordinates Mol file for the small molecule Search links Involved in 141 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline succinate Identifier CHEBI:30031 (CAS: 56-14-4) ^help_outline Charge -2 Formula C4H4O4 InChIKey^help_outline KDYFGRWQOYBRFD-UHFFFAOYSA-L SMILES^help_outline [O-]C(=O)CCC([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 340 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline CO₂ Identifier CHEBI:16526 (CAS: 124-38-9) ^help_outline Charge 0 Formula CO2 InChIKey^help_outline CURLTUGMZLYLDI-UHFFFAOYSA-N SMILES^help_outline O=C=O 2D coordinates Mol file for the small molecule Search links Involved in 1,032 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule

Cross-references

	RHEA:49524	RHEA:49525	RHEA:49526	RHEA:49527
Reaction direction	undefined	left-to-right	right-to-left	bidirectional
UniProtKB ^help_outline	10 proteins	6 proteins
EC numbers ^help_outline	1.14.11.51
Gene Ontology ^help_outline	GO:0141131
MetaCyc ^help_outline				RXN-17812

Publications

DNA methylation on N(6)-adenine in mammalian embryonic stem cells.

Wu T.P., Wang T., Seetin M.G., Lai Y., Zhu S., Lin K., Liu Y., Byrum S.D., Mackintosh S.G., Zhong M., Tackett A., Wang G., Hon L.S., Fang G., Swenberg J.A., Xiao A.Z.

It has been widely accepted that 5-methylcytosine is the only form of DNA methylation in mammalian genomes. Here we identify N(6)-methyladenine as another form of DNA modification in mouse embryonic stem cells. Alkbh1 encodes a demethylase for N(6)-methyladenine. An increase of N(6)-methyladenine ... >> More

It has been widely accepted that 5-methylcytosine is the only form of DNA methylation in mammalian genomes. Here we identify N(6)-methyladenine as another form of DNA modification in mouse embryonic stem cells. Alkbh1 encodes a demethylase for N(6)-methyladenine. An increase of N(6)-methyladenine levels in Alkbh1-deficient cells leads to transcriptional silencing. N(6)-methyladenine deposition is inversely correlated with the evolutionary age of LINE-1 transposons; its deposition is strongly enriched at young (<1.5 million years old) but not old (>6 million years old) L1 elements. The deposition of N(6)-methyladenine correlates with epigenetic silencing of such LINE-1 transposons, together with their neighbouring enhancers and genes, thereby resisting the gene activation signals during embryonic stem cell differentiation. As young full-length LINE-1 transposons are strongly enriched on the X chromosome, genes located on the X chromosome are also silenced. Thus, N(6)-methyladenine developed a new role in epigenetic silencing in mammalian evolution distinct from its role in gene activation in other organisms. Our results demonstrate that N(6)-methyladenine constitutes a crucial component of the epigenetic regulation repertoire in mammalian genomes. << Less

Nature 532:329-333(2016) [PubMed] [EuropePMC]

RHEA:49526 a 2'-deoxyadenosine in DNA + formaldehyde + succinate + CO2 => an N(6)-methyl-2'-deoxyadenosine in DNA + 2-oxoglutarate + O2 Reaction with net flow from right to left. help_outline

Reaction participants Show >> << Hide

Cross-references

Publications

DNA methylation on N(6)-adenine in mammalian embryonic stem cells.

RHEA:49526 a 2'-deoxyadenosine in DNA + formaldehyde + succinate + CO2 => an N(6)-methyl-2'-deoxyadenosine in DNA + 2-oxoglutarate + O2 Reaction with net flow from right to left. ^help_outline