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Literature summary for 4.1.1.116 extracted from
- STM2360 encodes a D-ornithine/D-lysine decarboxylase in Salmonella enterica serovar typhimurium (2017), Arch. Biochem. Biophys., 634, 83-87 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene STM2360, DNA and amino acid sequence determination and analysis, sequence comparisons, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3), the enzyme is unable to complement lysine auxotrophy in a lysA mutant | Salmonella enterica subsp. enterica serovar Typhimurium |
| gene STM2360, located in a small operon of undetermined function in Salmonella enterica serovar Typhimurium LT2, DNA and amino acid sequence determination and analysis, recombinant overexpression of C-terminally His-tagged enzyme in Escherichia coli strain BL21(DE3) | Salmonella enterica subsp. enterica serovar Typhimurium |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | kinetics for both D-lysine and D-ornithine are distinctly sigmoid, strong cooperative behaviour suggesting that there may be an allosteric site for effectors and/or oligomeric equilibria which affect activity, kinetic analysis, overview | Salmonella enterica subsp. enterica serovar Typhimurium | |
| additional information | - |
additional information | the kinetics for both D-lysine and D-ornithine are distinctly sigmoid, with n of about 3. The kinetic data is analyzed by fitting to the Hill equation | Salmonella enterica subsp. enterica serovar Typhimurium | |
| 4.12 | - |
D-ornithine | pH 7.0, 37°C, recombinant enzyme | Salmonella enterica subsp. enterica serovar Typhimurium |  |
| 4.13 | - |
D-ornithine | pH 7.0, 25°C, recombinant His-tagged enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | |
| 7.32 | - |
D-Lysine | pH 7.0, 37°C, recombinant enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | |
| 7.32 | - |
D-Lysine | pH 7.0, 25°C, recombinant His-tagged enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| D-ornithine | Salmonella enterica subsp. enterica serovar Typhimurium | - |
putrescine + CO2 | - |
? | |
| D-ornithine | Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 | - |
putrescine + CO2 | - |
? | |
| D-ornithine | Salmonella enterica subsp. enterica serovar Typhimurium LT2 | - |
putrescine + CO2 | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Salmonella enterica subsp. enterica serovar Typhimurium | Q8ZNC4 | - |
- |
| Salmonella enterica subsp. enterica serovar Typhimurium | Q8ZNC4 | Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 | - |
| Salmonella enterica subsp. enterica serovar Typhimurium LT2 | Q8ZNC4 | Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 | - |
| Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 | Q8ZNC4 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant C-terminally His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and ultrafiltration | Salmonella enterica subsp. enterica serovar Typhimurium |
| recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography | Salmonella enterica subsp. enterica serovar Typhimurium |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| D-lysine = cadaverine + CO2 | (1) | Salmonella enterica subsp. enterica serovar Typhimurium | |
| D-ornithine = putrescine + CO2 | (2) | Salmonella enterica subsp. enterica serovar Typhimurium |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| D-lysine | - |
Salmonella enterica subsp. enterica serovar Typhimurium | cadaverine + CO2 | - |
? | |
| D-lysine | - |
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 | cadaverine + CO2 | - |
? | |
| D-lysine | - |
Salmonella enterica subsp. enterica serovar Typhimurium LT2 | cadaverine + CO2 | - |
? | |
| D-ornithine | - |
Salmonella enterica subsp. enterica serovar Typhimurium | putrescine + CO2 | - |
? | |
| D-ornithine | - |
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 | putrescine + CO2 | - |
? | |
| D-ornithine | - |
Salmonella enterica subsp. enterica serovar Typhimurium LT2 | putrescine + CO2 | - |
? | |
| additional information | enzyme product identification by NMR and mass spectrometry. The D-lysine substrate is preferred over D-ornithine. pH-Indicator-based enzyme assay. No activity with D-arginine, L-arginine, L-lysine, or L-ornithine, and no activity with DL-2,4-diaminopropionic acid, D-methionine, D-leucine, D-glutamine, D-asparagine, D-phenylalanine, and D-valine. Transamination or decarboxylation-dependent transamination occurs with D-arginine to form pyridoxamine-5'-phosphate and inactive enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | ? | - |
? | |
| additional information | the protein coded by STM2360 has a catalytic activity as a D-ornithine/D-lysine decarboxylase (DOKDC), it is specific for D-amino acids. The reaction products, cadaverine and putrescine, respectively, are identified by NMR and mass spectrometry. The substrate specificity of enzyme DOKDC is D-lysine before D-ornithine. STM2358, located in the same operon, has ornithine racemase activity. Phenol red assay | Salmonella enterica subsp. enterica serovar Typhimurium | ? | - |
? | |
| additional information | enzyme product identification by NMR and mass spectrometry. The D-lysine substrate is preferred over D-ornithine. pH-Indicator-based enzyme assay. No activity with D-arginine, L-arginine, L-lysine, or L-ornithine, and no activity with DL-2,4-diaminopropionic acid, D-methionine, D-leucine, D-glutamine, D-asparagine, D-phenylalanine, and D-valine. Transamination or decarboxylation-dependent transamination occurs with D-arginine to form pyridoxamine-5'-phosphate and inactive enzyme | Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 | ? | - |
? | |
| additional information | the protein coded by STM2360 has a catalytic activity as a D-ornithine/D-lysine decarboxylase (DOKDC), it is specific for D-amino acids. The reaction products, cadaverine and putrescine, respectively, are identified by NMR and mass spectrometry. The substrate specificity of enzyme DOKDC is D-lysine before D-ornithine. STM2358, located in the same operon, has ornithine racemase activity. Phenol red assay | Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 | ? | - |
? | |
| additional information | enzyme product identification by NMR and mass spectrometry. The D-lysine substrate is preferred over D-ornithine. pH-Indicator-based enzyme assay. No activity with D-arginine, L-arginine, L-lysine, or L-ornithine, and no activity with DL-2,4-diaminopropionic acid, D-methionine, D-leucine, D-glutamine, D-asparagine, D-phenylalanine, and D-valine. Transamination or decarboxylation-dependent transamination occurs with D-arginine to form pyridoxamine-5'-phosphate and inactive enzyme | Salmonella enterica subsp. enterica serovar Typhimurium LT2 | ? | - |
? | |
| additional information | the protein coded by STM2360 has a catalytic activity as a D-ornithine/D-lysine decarboxylase (DOKDC), it is specific for D-amino acids. The reaction products, cadaverine and putrescine, respectively, are identified by NMR and mass spectrometry. The substrate specificity of enzyme DOKDC is D-lysine before D-ornithine. STM2358, located in the same operon, has ornithine racemase activity. Phenol red assay | Salmonella enterica subsp. enterica serovar Typhimurium LT2 | ? | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| D-Orn/D-Lys decarboxylase | - |
Salmonella enterica subsp. enterica serovar Typhimurium |
| D-ornithine/D-lysine decarboxylase | - |
Salmonella enterica subsp. enterica serovar Typhimurium |
| dokD | proposed gene name | Salmonella enterica subsp. enterica serovar Typhimurium |
| DOKDC | - |
Salmonella enterica subsp. enterica serovar Typhimurium |
| STM2360 | - |
Salmonella enterica subsp. enterica serovar Typhimurium |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 25 | - |
assay at | Salmonella enterica subsp. enterica serovar Typhimurium |
| 37 | - |
assay at | Salmonella enterica subsp. enterica serovar Typhimurium |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 1.8 | - |
D-ornithine | pH 7.0, 37°C, recombinant enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | |
| 1.8 | - |
D-ornithine | pH 7.0, 25°C, recombinant His-tagged enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | |
| 4.4 | - |
D-Lysine | pH 7.0, 37°C, recombinant enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | |
| 4.4 | - |
D-Lysine | pH 7.0, 25°C, recombinant His-tagged enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 6.5 | 8 | - |
Salmonella enterica subsp. enterica serovar Typhimurium |
| 7 | - |
assay at | Salmonella enterica subsp. enterica serovar Typhimurium |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| pyridoxal 5'-phosphate | - |
Salmonella enterica subsp. enterica serovar Typhimurium | |
| pyridoxal 5'-phosphate | dependent on | Salmonella enterica subsp. enterica serovar Typhimurium | |
Expression
| Organism | Comment | Expression |
|---|---|---|
| Salmonella enterica subsp. enterica serovar Typhimurium | levels of STM2360 transcripts are low and uninduced under all of the environmental conditions tested | additional information |
| Salmonella enterica subsp. enterica serovar Typhimurium | gene STM2361 is transcribed divergently from gene STM2360 and encodes a bEBP, which given its proximity, is likely responsible for activating transcription of the STM2360 operon. Transcription of STM2361 is induced 13fold by acid shock (exposure of the cells to pH 3 for 10 min) and 3fold by bile shock | up |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | the amino acid sequence of STM2360 shows significant similarity (about 30% identity) to diaminopimelate decarboxylase (DapDC), a fold III pyridoxal 5'-phosphate (PLP) dependent enzyme involved in L-lysine biosynthesis. Homologues of STM2360 with high sequence identity (over 80%) are found in other common enterobacteria, including species of Klebsiella, Citrobacter, Vibrio, and Hafnia, as well as Clostridium in the Firmicutes, and Pseudomonas | Salmonella enterica subsp. enterica serovar Typhimurium |
| evolution | the amino acid sequence of STM2360 shows significant similarity (about 30% identity) to diaminopimelate decarboxylase (DapDC, EC 4.1.1.20), a fold III pyridoxal-5'-phosphate (PLP) dependent enzyme involved in L-lysine biosynthesis. STM2358, located in the same operon, has ornithine racemase activity. This suggests that the physiological substrate of the decarboxylase and the operon is ornithine. STM2360 is annotated as encoding a second DapDC in Salmonella typhimurium LT2, although it is unable to complement lysine auxotrophy in a lysA mutant | Salmonella enterica subsp. enterica serovar Typhimurium |
| physiological function | the physiological substrate of the decarboxylase (and the operon) is ornithine. No role of DOKDC in relief of acid stress, but the enzyme enzyme plays an important role in microbial metabolism | Salmonella enterica subsp. enterica serovar Typhimurium |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.44 | - |
D-ornithine | pH 7.0, 37°C, recombinant enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | |
| 0.6 | - |
D-Lysine | pH 7.0, 37°C, recombinant enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | |
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