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Literature summary extracted from

  • Phillips, R.S.; Poteh, P.; Miller, K.A.; Hoover, T.R.
    STM2360 encodes a D-ornithine/D-lysine decarboxylase in Salmonella enterica serovar typhimurium (2017), Arch. Biochem. Biophys., 634, 83-87 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.1.1.116 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
4.1.1.116 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
5.1.1.12 gene STM2358, DNA and amino acid sequence determination and analysis, sequence comparisons, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) Salmonella enterica subsp. enterica serovar Typhimurium

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
4.1.1.116 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
4.1.1.116 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
4.1.1.116 4.12
-
D-ornithine pH 7.0, 37°C, recombinant enzyme Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 4.13
-
D-ornithine pH 7.0, 25°C, recombinant His-tagged enzyme Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 7.32
-
D-Lysine pH 7.0, 37°C, recombinant enzyme Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 7.32
-
D-Lysine pH 7.0, 25°C, recombinant His-tagged enzyme Salmonella enterica subsp. enterica serovar Typhimurium

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.1.1.116 D-ornithine Salmonella enterica subsp. enterica serovar Typhimurium
-
putrescine + CO2
-
?
4.1.1.116 D-ornithine Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
-
putrescine + CO2
-
?
4.1.1.116 D-ornithine Salmonella enterica subsp. enterica serovar Typhimurium LT2
-
putrescine + CO2
-
?
5.1.1.12 L-Ornithine Salmonella enterica subsp. enterica serovar Typhimurium preferred substrate D-Ornithine
-
r

Organism

EC Number Organism UniProt Comment Textmining
4.1.1.116 Salmonella enterica subsp. enterica serovar Typhimurium Q8ZNC4
-
-
4.1.1.116 Salmonella enterica subsp. enterica serovar Typhimurium Q8ZNC4 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2
-
4.1.1.116 Salmonella enterica subsp. enterica serovar Typhimurium LT2 Q8ZNC4 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2
-
4.1.1.116 Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 Q8ZNC4
-
-
5.1.1.12 Salmonella enterica subsp. enterica serovar Typhimurium Q8ZNC6
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.1.1.116 recombinant C-terminally His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and ultrafiltration Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography Salmonella enterica subsp. enterica serovar Typhimurium
5.1.1.12 recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography Salmonella enterica subsp. enterica serovar Typhimurium

Reaction

EC Number Reaction Comment Organism Reaction ID
4.1.1.116 D-lysine = cadaverine + CO2 (1) Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 D-ornithine = putrescine + CO2 (2) Salmonella enterica subsp. enterica serovar Typhimurium

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.1.1.116 D-lysine
-
Salmonella enterica subsp. enterica serovar Typhimurium cadaverine + CO2
-
?
4.1.1.116 D-lysine
-
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 cadaverine + CO2
-
?
4.1.1.116 D-lysine
-
Salmonella enterica subsp. enterica serovar Typhimurium LT2 cadaverine + CO2
-
?
4.1.1.116 D-ornithine
-
Salmonella enterica subsp. enterica serovar Typhimurium putrescine + CO2
-
?
4.1.1.116 D-ornithine
-
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 putrescine + CO2
-
?
4.1.1.116 D-ornithine
-
Salmonella enterica subsp. enterica serovar Typhimurium LT2 putrescine + CO2
-
?
4.1.1.116 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 ?
-
?
4.1.1.116 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 ?
-
?
4.1.1.116 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 ?
-
?
4.1.1.116 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 ?
-
?
4.1.1.116 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 ?
-
?
4.1.1.116 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 ?
-
?
5.1.1.12 L-arginine
-
Salmonella enterica subsp. enterica serovar Typhimurium D-arginine
-
r
5.1.1.12 L-lysine very low activity Salmonella enterica subsp. enterica serovar Typhimurium D-lysine
-
r
5.1.1.12 L-Ornithine preferred substrate Salmonella enterica subsp. enterica serovar Typhimurium D-Ornithine
-
r
5.1.1.12 additional information the recombinant gene STM2358 product has ornithine racemase activity, no measureable alanine racemase activity of the enzyme Salmonella enterica subsp. enterica serovar Typhimurium ?
-
?

Synonyms

EC Number Synonyms Comment Organism
4.1.1.116 D-Orn/D-Lys decarboxylase
-
Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 D-ornithine/D-lysine decarboxylase
-
Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 dokD proposed gene name Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 DOKDC
-
Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 STM2360
-
Salmonella enterica subsp. enterica serovar Typhimurium
5.1.1.12 STM2358
-
Salmonella enterica subsp. enterica serovar Typhimurium

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
4.1.1.116 25
-
assay at Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 37
-
assay at Salmonella enterica subsp. enterica serovar Typhimurium

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
4.1.1.116 1.8
-
D-ornithine pH 7.0, 37°C, recombinant enzyme Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 1.8
-
D-ornithine pH 7.0, 25°C, recombinant His-tagged enzyme Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 4.4
-
D-Lysine pH 7.0, 37°C, recombinant enzyme Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 4.4
-
D-Lysine pH 7.0, 25°C, recombinant His-tagged enzyme Salmonella enterica subsp. enterica serovar Typhimurium

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.1.1.116 6.5 8
-
Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 7
-
assay at Salmonella enterica subsp. enterica serovar Typhimurium

Cofactor

EC Number Cofactor Comment Organism Structure
4.1.1.116 pyridoxal 5'-phosphate
-
Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 pyridoxal 5'-phosphate dependent on Salmonella enterica subsp. enterica serovar Typhimurium
5.1.1.12 pyridoxal 5'-phosphate dependent on Salmonella enterica subsp. enterica serovar Typhimurium

Expression

EC Number Organism Comment Expression
4.1.1.116 Salmonella enterica subsp. enterica serovar Typhimurium levels of STM2360 transcripts are low and uninduced under all of the environmental conditions tested additional information
4.1.1.116 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

EC Number General Information Comment Organism
4.1.1.116 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
4.1.1.116 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
4.1.1.116 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
5.1.1.12 evolution a BLAST search using the translated amino acid sequence of STM2358 results in significant higher similarity (37% identity) with sequences of ornithine racemase than with alanine racemase (27% identity), suggesting that it may be an ornithine racemase Salmonella enterica subsp. enterica serovar Typhimurium

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
4.1.1.116 0.44
-
D-ornithine pH 7.0, 37°C, recombinant enzyme Salmonella enterica subsp. enterica serovar Typhimurium
4.1.1.116 0.6
-
D-Lysine pH 7.0, 37°C, recombinant enzyme Salmonella enterica subsp. enterica serovar Typhimurium