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Literature summary for 3.1.4.52 extracted from
- Escherichia coli K-12 YfgF is an anaerobic cyclic di-GMP phosphodiesterase with roles in cell surface remodelling and the oxidative stress response (2010), Microbiology, 156, 2873-2886.
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene yfgF is expressed under anaerobic conditions from a class II FNR, i.e. regulator of fumarate and nitrate reduction-dependent promoter | Escherichia coli |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| additional information | disruption in the yfgF gene by linear transformation, phenotype, overview. The mutant is more sensitive to stress than the parent strain | Escherichia coli |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| 5'-phosphoguanylyl-(3'-5')-guanosine | the cyclic di-GMP phosphodiesterase activity of YfgFGE and YfgFE is inhibited by the reaction product | Escherichia coli |  |
| Ca2+ | inhibits both YfgF GGDEF-EAL (YfgFGE) and EAL (YfgFE) domains | Escherichia coli | |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | required, best at 10 mM for both YfgF GGDEF-EAL (YfgFGE) and EAL (YfgFE) domains | Escherichia coli | |
| Mn2+ | required, best at 10 mM for both YfgF GGDEF-EAL (YfgFGE) and EAL (YfgFE) domains | Escherichia coli | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | Escherichia coli | purified YfgF GGDEF-EAL (YfgFGE) and EAL (YfgFE) domains possess cyclic di-GMP-specific phosphodiesterase activity, but lack diguanylate cyclase activity | ? | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Escherichia coli | - |
gene yfgF | - |
Source Tissue
| Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|
| additional information | anaerobic expression of yfgF is greatest in stationary phase, and in cultures grown at 28°C | Escherichia coli | - |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| cyclic di-3',5'-guanylate + H2O | - |
Escherichia coli | 5'-phosphoguanylyl(3'-5')guanosine | - |
? | |
| additional information | purified YfgF GGDEF-EAL (YfgFGE) and EAL (YfgFE) domains possess cyclic di-GMP-specific phosphodiesterase activity, but lack diguanylate cyclase activity | Escherichia coli | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| dimer | YfgFGE | Escherichia coli |
| monomer | YfgFE, the monomeric EAL domain can be active as phosphodiesterases | Escherichia coli |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| YfgF | - |
Escherichia coli |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 37 | - |
assay at | Escherichia coli |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7.5 | - |
YfgF GGDEF-EAL (YfgFGE) and EAL (YfgFE) domains | Escherichia coli |
Expression
| Organism | Comment | Expression |
|---|---|---|
| Escherichia coli | low growth rates promote yfgF expression | up |
General Information
| General Information | Comment | Organism |
|---|---|---|
| malfunction | mutation of yfgF results in altered cell surface properties and enhanced sensitivity when anaerobic cultures are exposed to peroxides | Escherichia coli |
| additional information | the catalytically inactive GGDEF domain is required for YfgFGE dimerization and enhanced cyclic di-GMP phosphodiesterase activity in the presence of physiological concentrations of Mg2+ | Escherichia coli |
| physiological function | anaerobic cyclic di-GMP phosphodiesterase is involved in remodelling the cell surface of Escherichia coli K-12 and in the response to peroxide shock, with implications for integrating three global regulatory networks, i.e. oxygen regulation, cyclic di-GMP signalling and the oxidative stress response. YfgF does possess diguanylatecyclase and/or phosphodiesterase activities, while purified YfgF GGDEF-EAL (YfgFGE) and EAL (YfgFE) domains possess cyclic di-GMP-specific phosphodiesterase activity, but lack diguanylate cyclase activity | Escherichia coli |
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