Escherichia coli K-12 substr. MG1655 Reaction:

Superclasses: Reactions Classified By Conversion Type Simple Reactions Chemical Reactions
Reactions Classified By Substrate Small-Molecule Reactions

EC Number:

Enzymes and Genes:
5'-deoxyribonucleotidase Inferred from experiment : ushA
CPS-53 (KpLE1) prophage; deoxyribonucleoside 5'-monophosphate phosphatase Inferred from experiment : yfdR
dCMP phosphohydrolase Inferred from experiment : yfbR
acid phosphatase / phosphotransferase Inferred from experiment : aphA

Reaction Locations: periplasmic space (sensu Gram-negative Bacteria), cytosol

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

Mass balance status: Balanced.

Instance reactions:
dAMP + H2O → 2'-deoxyadenosine + phosphate (

dGMP + H2O → 2'-deoxyguanosine + phosphate (

dCMP + H2O → 2'-deoxycytidine + phosphate (

dUMP + H2O → 2'-deoxyuridine + phosphate (

dTMP + H2O → thymidine + phosphate (

Direct generic reaction:
a nucleoside 5'-monophosphate[periplasmic space] + H2O[periplasmic space] → a nucleoside[periplasmic space] + phosphate[periplasmic space] (no EC#)

Enzyme Commission Primary Name: 5′-deoxynucleotidase

Enzyme Commission Synonyms: yfbR (gene name)

Enzyme Commission Summary:
The enzyme, characterized from the bacterium Escherichia coli, shows strict specificity towards deoxyribonucleoside 5'-monophosphates and does not dephosphorylate 5'-ribonucleotides or ribonucleoside 3'-monophosphates. A divalent metal cation is required for activity, with cobalt providing the highest activity.

Citations: [Proudfoot04, Zimmerman08]

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Instance reaction of [a nucleoside 5'-monophosphate[periplasmic space] + H2O[periplasmic space] → a nucleoside[periplasmic space] + phosphate[periplasmic space]] (no EC#):
i1: a 2'-deoxyribonucleoside 5'-monophosphate + H2O → a 2'-deoxynucleoside + phosphate (

Relationship Links: BRENDA:EC: , ENZYME:EC: , IUBMB-ExplorEnz:EC:


Proudfoot04: Proudfoot M, Kuznetsova E, Brown G, Rao NN, Kitagawa M, Mori H, Savchenko A, Yakunin AF (2004). "General enzymatic screens identify three new nucleotidases in Escherichia coli. Biochemical characterization of SurE, YfbR, and YjjG." J Biol Chem 279(52);54687-94. PMID: 15489502

Zimmerman08: Zimmerman MD, Proudfoot M, Yakunin A, Minor W (2008). "Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli." J Mol Biol 378(1);215-26. PMID: 18353368

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Fri Oct 9, 2015, biocyc13.