Rhea - reaction knowledgebase

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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 acetyl-CoA Identifier CHEBI:57288 (Beilstein: 8468140) ^help_outline Charge -4 Formula C23H34N7O17P3S InChIKey^help_outline ZSLZBFCDCINBPY-ZSJPKINUSA-J SMILES^help_outline CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP([O-])(=O)OP([O-])(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP([O-])([O-])=O)n1cnc2c(N)ncnc12 2D coordinates Mol file for the small molecule Search links Involved in 321 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline AH₂ Identifier CHEBI:17499 Charge 0 Formula RH2 SMILES^help_outline *([H])[H] 2D coordinates Mol file for the small molecule Search links Involved in 2,713 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline NH₄⁺ Identifier CHEBI:28938 (CAS: 14798-03-9) ^help_outline Charge 1 Formula H4N InChIKey^help_outline QGZKDVFQNNGYKY-UHFFFAOYSA-O SMILES^help_outline [H][N+]([H])([H])[H] 2D coordinates Mol file for the small molecule Search links Involved in 518 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 2,648 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline A Identifier CHEBI:13193 Charge Formula R SMILES^help_outline * 2D coordinates Mol file for the small molecule Search links Involved in 2,783 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name^help_outline a N⁶-methylcarbamoyl-2'-deoxyadenosine in DNA Identifier RHEA-COMP:16940 Reactive part ^help_outline
- Name ^help_outline N⁶-methylcarbamoyl-2'-deoxyadenosine 5'-monophosphate residue Identifier CHEBI:166827 Charge -1 Formula C12H14N6O6P SMILES^help_outline N(C1=NC=NC2=C1N=CN2[C@@H]3O[C@H](COP(=O)(*)[O-])[C@@H](O*)C3)CC(=O)N 2D coordinates Mol file for the small molecule Search links Involved in 1 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Search links Involved in 1 reaction(s) Find proteins in UniProtKB for this molecule
Name ^help_outline CoA Identifier CHEBI:57287 (Beilstein: 11604429) ^help_outline Charge -4 Formula C21H32N7O16P3S InChIKey^help_outline RGJOEKWQDUBAIZ-IBOSZNHHSA-J SMILES^help_outline CC(C)(COP([O-])(=O)OP([O-])(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP([O-])([O-])=O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCS 2D coordinates Mol file for the small molecule Search links Involved in 1,468 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline H⁺ Identifier CHEBI:15378 Charge 1 Formula H InChIKey^help_outline GPRLSGONYQIRFK-UHFFFAOYSA-N SMILES^help_outline [H+] 2D coordinates Mol file for the small molecule Search links Involved in 9,176 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline H₂O Identifier CHEBI:15377 (Beilstein: 3587155; CAS: 7732-18-5) ^help_outline Charge 0 Formula H2O InChIKey^help_outline XLYOFNOQVPJJNP-UHFFFAOYSA-N SMILES^help_outline [H]O[H] 2D coordinates Mol file for the small molecule Search links Involved in 6,048 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule

Cross-references

	RHEA:65948	RHEA:65949	RHEA:65950	RHEA:65951
Reaction direction	undefined	left-to-right	right-to-left	bidirectional
UniProtKB ^help_outline	2 proteins

Publications

Emergence of a novel immune-evasion strategy from an ancestral protein fold in bacteriophage Mu.

Karambelkar S., Udupa S., Gowthami V.N., Ramachandra S.G., Swapna G., Nagaraja V.

The broad host range bacteriophage Mu employs a novel 'methylcarbamoyl' modification to protect its DNA from diverse restriction systems of its hosts. The DNA modification is catalyzed by a phage-encoded protein Mom, whose mechanism of action is a mystery. Here, we characterized the co-factor and ... >> More

The broad host range bacteriophage Mu employs a novel 'methylcarbamoyl' modification to protect its DNA from diverse restriction systems of its hosts. The DNA modification is catalyzed by a phage-encoded protein Mom, whose mechanism of action is a mystery. Here, we characterized the co-factor and metal-binding properties of Mom and provide a molecular mechanism to explain 'methylcarbamoyl'ation of DNA by Mom. Computational analyses revealed a conserved GNAT (GCN5-related N-acetyltransferase) fold in Mom. We demonstrate that Mom binds to acetyl CoA and identify the active site. We discovered that Mom is an iron-binding protein, with loss of Fe2+/3+-binding associated with loss of DNA modification activity. The importance of Fe2+/3+ is highlighted by the colocalization of Fe2+/3+ with acetyl CoA within the Mom active site. Puzzlingly, acid-base mechanisms employed by >309,000 GNAT members identified so far, fail to support methylcarbamoylation of adenine using acetyl CoA. In contrast, free-radical chemistry catalyzed by transition metals like Fe2+/3+ can explain the seemingly challenging reaction, accomplished by collaboration between acetyl CoA and Fe2+/3+. Thus, binding to Fe2+/3+, a small but unprecedented step in the evolution of Mom, allows a giant chemical leap from ordinary acetylation to a novel methylcarbamoylation function, while conserving the overall protein architecture. << Less

Nucleic Acids Res. 48:5294-5305(2020) [PubMed] [EuropePMC]

Comments

The precise donor of the ammonium donor is not known. Likewise, the need for O2>/smallsub> has not been experimentally verified.

RHEA:65950 A + a N(6)-methylcarbamoyl-2'-deoxyadenosine in DNA + CoA + H(+) + 2 H2O => a 2'-deoxyadenosine in DNA + acetyl-CoA + AH2 + NH4(+) + O2 Reaction with net flow from right to left. help_outline

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Cross-references

Publications

Emergence of a novel immune-evasion strategy from an ancestral protein fold in bacteriophage Mu.

Comments

RHEA:65950 A + a N(6)-methylcarbamoyl-2'-deoxyadenosine in DNA + CoA + H(+) + 2 H2O => a 2'-deoxyadenosine in DNA + acetyl-CoA + AH2 + NH4(+) + O2 Reaction with net flow from right to left. ^help_outline