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Information on EC 4.1.1.116 - D-ornithine/D-lysine decarboxylase
for references in articles please use BRENDA:EC4.1.1.116
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EC Tree 4 Lyases
4.1 Carbon-carbon lyases
4.1.1 Carboxy-lyases
4.1.1.116 D-ornithine/D-lysine decarboxylase
IUBMB Comments
The enzyme, characterized from the bacterium Salmonella typhimurium LT2, is specific for D-ornithine and D-lysine. Requires pyridoxal 5′-phosphate.
The expected taxonomic range for this enzyme is: Salmonella enterica subsp. enterica serovar Typhimurium
showSynonyms
dokdc, stm2360, d-ornithine/d-lysine decarboxylase, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
D-Orn/D-Lys decarboxylase
D-ornithine/D-lysine decarboxylase
D-ornithine/lysine decarboxylase
dokD
DOKDC
STM2360
D-Orn/D-Lys decarboxylase
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
-
-
D-ornithine/D-lysine decarboxylase
-
D-ornithine/D-lysine decarboxylase
-
-
D-ornithine/D-lysine decarboxylase
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
-
-
D-ornithine/lysine decarboxylase
-
D-ornithine/lysine decarboxylase
-
-
dokD
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
proposed gene name
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
D-lysine = cadaverine + CO2
(1)
D-lysine = cadaverine + CO2
(1)
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
-
-
D-lysine = cadaverine + CO2
-
-
-
-
D-ornithine = putrescine + CO2
(2)
D-ornithine = putrescine + CO2
(2)
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
-
-
D-ornithine = putrescine + CO2
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
D-ornithine/D-lysine carboxy-lyase
The enzyme, characterized from the bacterium Salmonella typhimurium LT2, is specific for D-ornithine and D-lysine. Requires pyridoxal 5'-phosphate.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
D-lysine
cadaverine + CO2
Substrates: -
Products: -
Products: -
?
D-lysine
cadaverine + CO2
Substrates: -
Products: -
Products: -
?
D-lysine
cadaverine + CO2
Substrates: -
Products: -
Products: -
?
D-lysine
cadaverine + CO2
Substrates: -
Products: -
Products: -
?
D-lysine
cadaverine + CO2
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
Substrates: -
Products: -
Products: -
?
D-ornithine
putrescine + CO2
Substrates: -
Products: -
Products: -
?
D-ornithine
putrescine + CO2
Substrates: -
Products: -
Products: -
?
D-ornithine
putrescine + CO2
Substrates: -
Products: -
Products: -
?
D-ornithine
putrescine + CO2
Substrates: -
Products: -
Products: -
?
D-ornithine
putrescine + CO2
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
Substrates: -
Products: -
Products: -
?
additional information
?
-
Substrates: 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
Products: -
Products: -
?
additional information
?
-
-
Substrates: 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
Products: -
Products: -
?
additional information
?
-
Substrates: 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
Products: -
Products: -
?
additional information
?
-
-
Substrates: 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
Products: -
Products: -
?
additional information
?
-
Substrates: 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
Products: -
Products: -
?
additional information
?
-
Substrates: 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
Products: -
Products: -
?
additional information
?
-
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
Substrates: 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
Products: -
Products: -
?
additional information
?
-
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
Substrates: 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
Products: -
Products: -
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
D-lysine
cadaverine + CO2
Substrates: -
Products: -
Products: -
?
D-lysine
cadaverine + CO2
Substrates: -
Products: -
Products: -
?
D-ornithine
putrescine + CO2
Substrates: -
Products: -
Products: -
?
D-ornithine
putrescine + CO2
Substrates: -
Products: -
Products: -
?
D-ornithine
putrescine + CO2
Substrates: -
Products: -
Products: -
?
D-ornithine
putrescine + CO2
Substrates: -
Products: -
Products: -
?
D-ornithine
putrescine + CO2
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
Substrates: -
Products: -
Products: -
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
dependent on
pyridoxal 5'-phosphate
substrates bind to form external aldimine complexes with the pyridoxal-5'-phosphate with lambdamax 425 nm
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
7.32
D-Lysine
pH 7.0, 37°C, recombinant enzyme
7.32
D-Lysine
pH 7.0, 25°C, recombinant His-tagged enzyme
4.12
D-ornithine
pH 7.0, 37°C, recombinant enzyme
4.13
D-ornithine
pH 7.0, 25°C, recombinant His-tagged enzyme
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
-
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
-
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
-
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
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4.4
D-Lysine
pH 7.0, 37°C, recombinant enzyme
4.4
D-Lysine
pH 7.0, 25°C, recombinant His-tagged enzyme
1.8
D-ornithine
pH 7.0, 37°C, recombinant enzyme
1.8
D-ornithine
pH 7.0, 25°C, recombinant His-tagged enzyme
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.6
D-Lysine
pH 7.0, 37°C, recombinant enzyme
0.44
D-ornithine
pH 7.0, 37°C, recombinant enzyme
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
brenda
Salmonella enterica subsp. enterica serovar Typhimurium strain LT2
UniProt
brenda
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
-
UniProt
brenda
Salmonella enterica subsp. enterica serovar Typhimurium strain LT2
UniProt
brenda
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
physiological function
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
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
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
-
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
-
evolution
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
-
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
-
evolution
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
-
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
-
metabolism
enzyme catalyzes decarboxylation with inversion of stereochemistry. A concerted mechanism is supported by the lack of detectable exchange of the alpha-hydrogens of putrescine upon incubation with DOKDC in D2O
metabolism
-
enzyme catalyzes decarboxylation with inversion of stereochemistry. A concerted mechanism is supported by the lack of detectable exchange of the alpha-hydrogens of putrescine upon incubation with DOKDC in D2O
-
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
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
-
physiological function
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
-
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
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). DOKDC_SALTY
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
465
0
52598
Swiss-Prot
other Location (Reliability: 3)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, using 28-30% (w/v) dioxane
structure at 1.72 A resolution. The pyridoxal 5'-phosphate-binding lysine is located on the re-face of the pyridoxal 5'-phosphate
structures of mutant Y430F bound to HEPES, putrescine, D-ornithine, D-lysine, and D-arginine. The D-amino acids bind in the crystals to form equilibrium mixtures of gem-diamine and external aldimine complexes. An allosteric product activator site for putrescine is located on the 2fold axis between the two active sites. Putrescine binds by donating hydrogen bonds from the ammonium groups to Asp-361 and Gln-358 in the specificity helix of both chains. Glu-181 can form additional hydrogen bonds with the bound putrescine
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Y430F
Y430F
contratry to wild-type, mutant has measurable decarboxylase activity with both D- and L-lysine and ornithine. Addition of 0.1-1 mM putrescine eliminates the lag in steady state kinetics and abolishes the sigmoid kinetics
Y430F
-
contratry to wild-type, mutant has measurable decarboxylase activity with both D- and L-lysine and ornithine. Addition of 0.1-1 mM putrescine eliminates the lag in steady state kinetics and abolishes the sigmoid kinetics
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant C-terminally His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and ultrafiltration
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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)
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
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
levels of STM2360 transcripts are low and uninduced under all of the environmental conditions tested
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
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
-
-
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
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
-
-
levels of STM2360 transcripts are low and uninduced under all of the environmental conditions tested
levels of STM2360 transcripts are low and uninduced under all of the environmental conditions tested
-
-
levels of STM2360 transcripts are low and uninduced under all of the environmental conditions tested
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720
-
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Phillips, R.S.; Poteh, P.; Miller, K.A.; Hoover, T.R.
STM2360 encodes a D-ornithine/D-lysine decarboxylase in Salmonella enterica serovar typhimurium
Arch. Biochem. Biophys.
634
83-87
2017
Salmonella enterica subsp. enterica serovar Typhimurium (Q8ZNC4), Salmonella enterica subsp. enterica serovar Typhimurium, Salmonella enterica subsp. enterica serovar Typhimurium LT2 (Q8ZNC4), Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 (Q8ZNC4)
brenda
Phillips, R.S.; Poteh, P.; Krajcovic, D.; Miller, K.A.; Hoover, T.R.
Crystal sructure of D-ornithine/D-lysine decarboxylase, a stereoinverting decarboxylase Implications for substrate specificity and stereospecificity of fold III decarboxylases
Biochemistry
58
1038-1042
2019
Salmonella enterica subsp. enterica serovar Typhimurium, Salmonella enterica subsp. enterica serovar Typhimurium (Q8ZNC4), Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 (Q8ZNC4)
brenda
Phillips, R.S.; Nguyen Hoang, K.N.
The Y430F mutant of Salmonella D-ornithine/D-lysine decarboxylase has altered stereospecificity and a putrescine allosteric activation site
Arch. Biochem. Biophys.
731
109429
2022
Salmonella enterica subsp. enterica serovar Typhimurium (Q8ZNC4), Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 (Q8ZNC4)
brenda
EXTERNAL LINKS (specific for EC-Number 4.1.1.116)
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