Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014

Escherichia coli K-12 substr. MG1655 Enzyme: CPS-53 (KpLE1) prophage; deoxyribonucleoside 5'-monophosphate phosphatase

Gene: yfdR Accession Numbers: G7230 (EcoCyc), b2361, ECK2355

Regulation Summary Diagram: ?

YfdR is a deoxyribonucleoside 5'-monophosphate phosphatase with a conserved HD domain. The enzyme has a broader substrate range than YfbR [Zimmerman08].

Locations: cytosol

Map Position: [2,473,006 -> 2,473,542] (53.3 centisomes)
Length: 537 bp / 178 aa

Molecular Weight of Polypeptide: 20.255 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007791 , EchoBASE:EB3892 , EcoGene:EG14140 , EcoliWiki:b2361 , OU-Microarray:b2361 , PortEco:yfdR , Pride:P76514 , Protein Model Portal:P76514 , RefSeq:NP_416862 , RegulonDB:G7230 , SMR:P76514 , String:511145.b2361 , UniProt:P76514

Relationship Links: InterPro:IN-FAMILY:IPR003607 , InterPro:IN-FAMILY:IPR006674 , Smart:IN-FAMILY:SM00471

Gene-Reaction Schematic: ?

Instance reactions of [a 2'-deoxyribonucleoside 5'-monophosphate + H2O → a 2'-deoxynucleoside + phosphate] (
i1: dTMP + H2O → thymidine + phosphate (

i2: dAMP + H2O → 2'-deoxyadenosine + phosphate (

i3: dCMP + H2O → 2'-deoxycytidine + phosphate (

i4: dGMP + H2O → 2'-deoxyguanosine + phosphate (

i5: dUMP + H2O → 2'-deoxyuridine + phosphate (

GO Terms:

Biological Process: GO:0016311 - dephosphorylation Inferred from experiment [Zimmerman08]
Molecular Function: GO:0008252 - nucleotidase activity Inferred from experiment [Zimmerman08]
GO:0050897 - cobalt ion binding Inferred from experiment [Zimmerman08]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [Diaz-Mejia et al., 2009]

MultiFun Terms: extrachromosomal prophage genes and phage related functions

Essentiality data for yfdR knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes et al., 2003, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba et al., 2006, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce et al., 2006, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba et al., 2006, Comment 2]

Last-Curated ? 14-Oct-2013 by Keseler I , SRI International

Enzymatic reaction of: deoxyribonucleoside 5'-monophosphate phosphatase

EC Number:

a 2'-deoxyribonucleoside 5'-monophosphate + H2O <=> a 2'-deoxynucleoside + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for a 2'-deoxyribonucleoside 5'-monophosphate: dTMP [Zimmerman08 ] , dIMP [Zimmerman08 ] , dAMP [Zimmerman08 ] , dGMP [Zimmerman08 ] , dUMP [Zimmerman08 ] , dCMP [Zimmerman08 ] , GMP [Zimmerman08 ]

The KM for Co2+, determined using 0.5 mM dAMP as substrate, is 340 µM [Zimmerman08].

Cofactors or Prosthetic Groups: Co2+ [Zimmerman08]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Vmax (µmol mg-1 min-1)

Gene Local Context (not to scale): ?

Transcription Unit:


Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Baba et al., 2006: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Diaz-Mejia et al., 2009: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes et al., 2003: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Joyce et al., 2006: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

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

Report Errors or Provide Feedback
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 18.5 on Thu Dec 18, 2014, biocyc11.