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Mode of Action (MoA)
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synthesises hydroxymethyl-deoxycytidine triphosphate (Hm-dCTP) from Hm-dCMP.
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Evidence
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Deoxynucleoside monophosphate kinase (DNK) was functionally validated as an active kinase through structural, biochemical, and comparative analyses. DNK was overexpressed, purified, and crystallized in both binary (DNK–dGMP) and ternary (DNK–dGMP–ATP) complexes, enabling direct observation of substrate binding (ECO_0001823). Crystallographic data revealed well-defined interactions between DNK and dGMP, including specific hydrogen bonds at the base, sugar, and phosphate groups, confirming nucleotide recognition. ATP binding was also structurally resolved, and although β- and γ-phosphates were disordered, modeling based on homologous structures indicated a catalytically competent P-loop conformation. The arrangement of active site residues and the requirement for domain closure to bring phosphates into proximity supported a mechanism of phosphoryl transfer. Furthermore, DNK specificity for dGMP, dTMP, and hmdCMP was supported by kinetic studies and structure-based rationalization of hydrogen bond patterns that exclude non-substrate nucleotides. Mutation data cited (e.g., His206Q inactivation) corroborated the functional importance of residues involved in catalysis. Involved in modification of 5-hydroxymethyl-dCMP.
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MoA Category
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modifies phage molecules to avoid recognition
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Subtype(s) of the defence system(s) inhibited by the protein
Defence Subtype
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Escherichia coli RM
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Relevant publication(s)
DOI
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PMID: 8670851 (there is no DOI)
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Other components of the anti-defence system
Multicomponent System
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dcmp_hm;
bgt
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Known structure in PDB
PDB ID
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1DEK_A
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Genome(s) encoding the protein
Protein Source
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Enterobacteria phage T4
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Defence system(s) inhibited by the protein
Defences
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RM
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View homologs from eukaryotic dsDNA viruses
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