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Literature summary for 3.4.21.B30 extracted from
- Dimer exchange and cleavage specificity of the DNA damage response protein UmuD (2013), Biochim. Biophys. Acta, 1834, 611-620.
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| C24A | site-directed mutagenesis, that removes the cleavage site Cys residue of UmuD, the mutation does not substantially affect UmuD function, cleavage site variant | Escherichia coli |
| C25D | site-directed mutagenesis, that removes the cleavage site Cys residue of UmuD, the mutation does not substantially affect UmuD function, cleavage site variant. For cleavage to occur, UmuD UmuD G25D dimer must first exchange in the presence of RecA:ssDNA, and any cleavage detected results from cleavage in trans. Cleavage is less efficient in this context, indicating that the decreased rate of cleavage in the trans dimers results from the time required for dimer exchange to first take place before cleavage can occur | Escherichia coli |
| G92C | site-directed mutagenesis of of UmuD' | Escherichia coli |
| N41D | site-directed mutagenesis, the monomeric UmuD N41D variant can only cleave in the cis conformation | Escherichia coli |
| S60A | site-directed mutagenesis, a non-cleavable mutant of UmuD and UmuD', inactive active site mutant. For cleavage to occur, UmuD S60A dimer must first exchange in the presence of RecA:ssDNA, and any cleavage detected results from cleavage in trans. Cleavage is less efficient in this context, indicating that the decreased rate of cleavage in the trans dimers results from the time required for dimer exchange to first take place before cleavage can occur | Escherichia coli |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| UmuD2 + H2O | Escherichia coli | slow auto-cleavage of UmuD2 to UmuD'2 | UmuD2' + ? | - |
? |  |
| UmuD2 + H2O | Escherichia coli AB1157 | slow auto-cleavage of UmuD2 to UmuD'2 | UmuD2' + ? | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Escherichia coli | - |
gene umuD | - |
| Escherichia coli AB1157 | - |
gene umuD | - |
Posttranslational Modification
| Posttranslational Modification | Comment | Organism |
|---|---|---|
| proteolytic modification | slow auto-cleavage of UmuD2 to UmuD'2, the heterodimer efficiently cleaves to form UmuD'2 | Escherichia coli |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| UmuD2 + H2O | slow auto-cleavage of UmuD2 to UmuD'2 | Escherichia coli | UmuD2' + ? | - |
? | |
| UmuD2 + H2O | slow auto-cleavage of UmuD2 to UmuD'2. The wild-type UmuD homodimer cleaves in both cis and trans conformations | Escherichia coli | UmuD2' + ? | - |
? | |
| UmuD2 + H2O | slow auto-cleavage of UmuD2 to UmuD'2 | Escherichia coli AB1157 | UmuD2' + ? | - |
? | |
| UmuD2 + H2O | slow auto-cleavage of UmuD2 to UmuD'2. The wild-type UmuD homodimer cleaves in both cis and trans conformations | Escherichia coli AB1157 | UmuD2' + ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| dimer | UmuD dimers exchange readily, and the subunits of UmuD2 and UmuD'2 exchange to form the UmuDD' heterodimer. The heterodimer is the preferred but not exclusive protein form, and both the heterodimer and homodimers exhibit slow exchange kinetics, which is further inhibited in the presence of interacting partner DinB | Escherichia coli |
| More | UmuD proteins are shown to adopt multiple conformations in solution. UmuD contains only one cysteine (residue 24) per monomer at the cleavage site, which is between residues C24 and G25, cleavage of UmuD to form UmuD? removes the N-terminal 24 amino acids, which includes residue C24 | Escherichia coli |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| DNA damage response protein | - |
Escherichia coli |
| UmuD | - |
Escherichia coli |
| UmuD2 | - |
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 | - |
assay at | Escherichia coli |
Expression
| Organism | Comment | Expression |
|---|---|---|
| Escherichia coli | the enzyme is expressed shortly after the induction of the SOS response | up |
General Information
| General Information | Comment | Organism |
|---|---|---|
| malfunction | for cleavage to occur, UmuD S60A and UmuD G25D mutant dimers must first exchange in the presence of RecA:ssDNA, and any cleavage detected results from cleavage in trans. Cleavage is less efficient in this context, indicating that the decreased rate of cleavage in the trans dimers results from the time required for dimer exchange to first take place before cleavage can occur | Escherichia coli |
| additional information | UmuD proteins are shown to adopt multiple conformations in solution, homology models of UmuD and the structure of UmuD', overview. The heterodimer is the predominant UmuD protein conformer | Escherichia coli |
| physiological function | The umuD gene products perform distinct functions in preventing and facilitating mutagenesis. The full-length dimeric UmuD2 is the initial product that is expressed shortly after the induction of the SOS response and inhibits bacterial mutagenesis, allowing for error-free repair to occur. The slow auto-cleavage of UmuD2 to UmuD'2 promotes mutagenesis to ensure cell survival. The intracellular levels of UmuD2 and UmuD?2 are further regulated by degradation in vivo, returning the cell to a nonmutagenic state. Dynamic regulatory roles of the umuD gene, overview. UmuD lifecycle involves dimer exchange and cleavage in the regulation of the DNA damage respons | Escherichia coli |
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