Information on EC 3.5.1.104 - peptidoglycan-N-acetylglucosamine deacetylase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
3.5.1.104
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RECOMMENDED NAME
GeneOntology No.
peptidoglycan-N-acetylglucosamine deacetylase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
peptidoglycan-N-acetyl-D-glucosamine + H2O = peptidoglycan-D-glucosamine + acetate
show the reaction diagram
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-
-
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SYSTEMATIC NAME
IUBMB Comments
peptidoglycan-N-acetylglucosamine amidohydrolase
Modification of peptidoglycan by N-deacetylation is an important factor in virulence of Helicobacter pylori, Listeria monocytogenes and Streptococcus suis [4-6]. The enzyme from Streptococcus pneumoniae is a metalloenzyme using a His-His-Asp zinc-binding triad with a nearby aspartic acid and histidine acting as the catalytic base and acid, respectively [3].
CAS REGISTRY NUMBER
COMMENTARY hide
75217-01-5
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
gene pdaC
-
-
Manually annotated by BRENDA team
gene pdaC
-
-
Manually annotated by BRENDA team
gene hp0310
UniProt
Manually annotated by BRENDA team
IL1403
-
-
Manually annotated by BRENDA team
gene Rv1096
UniProt
Manually annotated by BRENDA team
gene Rv1096
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
4-methylumbelliferyl acetate + H2O
4-methylumbelliferol + acetate
show the reaction diagram
-
-
-
-
?
4-nitrophenyl acetate + H2O
4-nitrophenol + acetate
show the reaction diagram
-
-
-
-
?
acetylated peptidoglycan + H2O
deacetylated peptidoglycan + acetate
show the reaction diagram
GlcNAc-beta-1,4-GlcNAc + H2O
?
show the reaction diagram
-
no deacetylation of the reducing GlcNAc residue
-
-
?
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc + H2O
?
show the reaction diagram
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deacetylates all GlcNAc residues of the oligomer except the reducing end ones
-
-
?
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc + H2O
GlcNAc-beta-1,4-GlcN-beta-1,4-GlcNAc + acetate
show the reaction diagram
-
-
-
?
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc + H2O
?
show the reaction diagram
-
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc is the favorable substrate. Deacetylates all GlcNAc residues of the oligomer except the reducing end ones
-
-
?
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc + H2O
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcN-beta-1,4-GlcNAc + acetate
show the reaction diagram
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc + H2O
?
show the reaction diagram
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deacetylates all GlcNAc residues of the oligomer except the reducing end ones
-
-
?
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc + H2O
?
show the reaction diagram
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deacetylates all GlcNAc residues of the oligomer except the reducing end ones
-
-
?
GlcNAc-Mur[-L-Ala-D-Glu]-GlcNAc-MurNAcr[-L-Ala-D-Glu] + H2O
?
show the reaction diagram
GlcNAcbeta(1-4)GlcNAcbeta(1-4)GlcNAcbeta(1-4)GlcNAcbeta(1-4)GlcNAcbeta(1-4)GlcNAc + H2O
GlcNbeta(1-4)GlcNbeta(1-4)GlcNbeta(1-4)GlcNbeta(1-4)GlcNbeta(1-4)GlcNAc
show the reaction diagram
-
-
-
?
glycolchitin + H2O
?
show the reaction diagram
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poor substrate
-
-
?
N,N,N,N,N-pentaacetylchitopentaose + H2O
N,N,N-triacetylchitopentaose + N,N-diacetylchitopentaose + N-acetylchitopentaose + acetate
show the reaction diagram
-
-
almost quantitative conversion to mono-, di- and tri-de-acetylated products
-
?
peptidoglycan + H2O
?
show the reaction diagram
-
-
-
-
-
peptidoglycan from Streptococcus suis + H2O
deacetylated peptidoglycan + acetate
show the reaction diagram
-
-
-
-
?
peptidoglycan from wild-type Streptococcus pneumoniae + H2O
deacetylated peptidoglycan + acetate
show the reaction diagram
-
-
-
-
?
peptidoglycan-N-acetyl-D-glucosamine + H2O
peptidoglycan-D-glucosamine + acetate
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
acetylated peptidoglycan + H2O
deacetylated peptidoglycan + acetate
show the reaction diagram
peptidoglycan-N-acetyl-D-glucosamine + H2O
peptidoglycan-D-glucosamine + acetate
show the reaction diagram
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
-
activates
Fe2+
abolishes the acnB-pgdA transcript binding leading to destabilization of the enzyme's mRNA
Mg2+
-
activates
Mn2+
-
best activating metal ion
Ni2+
-
activates
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-[[4-(diethylamino)-2-hydroxyphenyl]carbonyl]benzoic acid
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1 mM, 7% residual activity
N-(3-acetylphenyl)-2-[2-(hydrazinylcarbonothioyl)hydrazinyl]-2-(1-oxido-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl)acetamide
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1 mM, 29% residual activity
additional information
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the enzyme mutant is sensitive to lysozyme, the growth rate is decreased
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
16.7
4-nitrophenyl acetate
-
37C, pH 7.0
2.27 - 2.38
4-yethylumbelliferyl acetate
3.9 - 4.1
GlcNAc-beta-1,4-GlcNAc
2.2 - 26
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc
1.18 - 12.3
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc
0.37 - 0.5
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc
0.3 - 0.45
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc
0.91 - 4.8
peptidoglycan-N-acetyl-D-glucosamine
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.46
4-nitrophenyl acetate
Streptococcus pneumoniae
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37C, pH 7.0
0.28 - 1.64
4-yethylumbelliferyl acetate
0.27 - 1.6
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc
0.24
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc
Bacillus subtilis
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pH 7.0, 37C
0.099 - 0.32
peptidoglycan-N-acetyl-D-glucosamine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0288
4-nitrophenyl acetate
Streptococcus pneumoniae
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37C, pH 7.0
418
0.129 - 0.71
4-yethylumbelliferyl acetate
1640
1.088
peptidoglycan-N-acetyl-D-glucosamine
Mycobacterium tuberculosis
O53444
recombinant enzyme, pH 7.0, 37C
67021
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.13
2-[[4-(diethylamino)-2-hydroxyphenyl]carbonyl]benzoic acid
Streptococcus pneumoniae
-
37C, pH 7.0
0.584
N-(3-acetylphenyl)-2-[2-(hydrazinylcarbonothioyl)hydrazinyl]-2-(1-oxido-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl)acetamide
Streptococcus pneumoniae
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37C, pH 7.0
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
Q97PW1
competition experiments with wild-type and mutant strains in lysozyme M-sufficient mice, effect of peptidoglycan modifying enzymes on growth, viability and hydrolysis of pneumococcal cell walls as well as on relative fitness during murine colonization in the presence or absence of lysozyme shown, contribution of lysozyme from neutrophils to survival and colonization of mutants lacking peptidoglycan modifications, effect of peptidoglycan modifying enzymes on expression of capsular polysaccharide (CPS)
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6
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enzyme BC1960
8
-
enzyme BC3618
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
-
enzyme BC1960
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
Q97PW1
peptidoglycan modifications during colonizing the mucosal surface of the upper respiratory tract, lysozyme M-sufficient mice
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
53000
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x * 53000, recombinant truncated enzyme, SDS-PAGE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homotetramer
tetramer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapour diffusion method; hanging-drop vapour diffusion method, enzyme is crystallized in the presence of (GlcNAc)6
purified recombinant N-terminally His6-tagged enzyme, vapor diffusion technique, mixing of 18 mg/ml protein solution with 0.2 M ammonium sulfate, 0.1 M tris sodium citrate, pH 5.6, and 15% w/v PEG 4000, 20C, X-ray diffraction structure determination and analysis at 2.2 A resolution; purified recombinant N-terminally His6-tagged enzyme, vapor diffusion technique, mixing of 18 mg/ml protein solution with precipitant solution containing 0.2 M ammonium sulfate, 0.1 M tris sodium citrate, pH 5.6, and 15% w/v PEG 4000, 20C, X-ray diffraction structure determination and analysis at 2.2 A resolution, molecular replacement and modeling
to 2.57 A resolution. The polypeptide folds into a single domain, characterized by a non-canonical TIM-barrel fold. Nine beta-strands are arranged in a central barrel surrounded by six alpha-helices. Four monomers are present in the asymmetric unit, arranged around a four-fold rotation axis
sitting-drop vapor diffusion method, native crystal structure and product complexes of SpPgdA
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
-
enzyme BC1960 retains 95% of its activity after 24 h; enzyme BC3618 is inactivated after 1h
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hexa-His-tagged form of PgdA
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partial AHU 1030
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recombinant His-tagged truncated enzyme from Escherichia coli strain JM109 by affinity chromatography and dialysis
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recombinant N-terminally His6-tagged enzyme
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cloning of pgdA on a multicopy plasmid vector results in an increased degree of peptidoglycan deacetylation
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expressed in Escherichia coli; expression in Escherichia coli
expression in Escherichia coli
gene ba1977; gene ba2944
gene bc1960; gene bc3618
gene hp0310, expression as N-terminally His6-tagged enzyme; gene hp0310, sequence comparison, recombinant expression of N-terminally His6-tagged enzyme
gene pdcA, overexpression of His-tagged truncated enzyme, lacking the transmembrane region, in Escherichia coli strain JM109, subcloning in Escherichia coli strain C600
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gene pgdA, in the wild type, pgdAmRNAhalf-life is 13 min, whereas the half-life for the acnB strain is 7 min, apo-AcnB binds to the 3'-untranslated region of the pgdA RNA transcript. AcnB-pgdA transcript binding is abolished by the addition of iron. Real-time quantitative PCR enzyme expression analysis and RNA footprinting
gene Rv1096, sequence comparisons, recombinant expression in Escherichia coli strain ER2566 and in Mycobacterium smegmatis strain mc2155, deacetylation of cell wall peptidoglycan by the recombinant enzyme leads to lysozyme resistance in Mycobacterium smegmatis
generation of mutant (pgdA and pgdAadr) and revertant strains
Q97PW1
the gene bc1960 is cloned and expressed in Escherichia coli; the gene bc3618 is cloned and expressed in Escherichia coli
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
expression of the pgdA gene is increased upon interaction of the bacterium with neutrophils in vitro as well as in vivo in experimentally inoculated mice
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HP310 is markedly up-expressed upon cell exposure to oxidative stress
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PgdA is highly expressed under oxidative stress
SfPgdA expression is controlled by PhoP, a phoP mutant does not produce SfPgdA, which results in increased sensitivity to lysozyyme
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SfPgdA expression is enhanced under low magnesium concentration
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H120F
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mutation impairs enzymic function
H125F
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mutation impairs enzymic function
L222V
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mutant exhibits sensitivity to lysozyme similar to wild-type, acticity is similar to wild-type
I419G
kcat/Km is 15fold lower than wild-type value
K304I
kcat/Km is 1.7fold higher than wild-type value
L302A
kcat/Km is 2.5fold higher than wild-type value
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
pharmacology
Q97PW1
studies on peptidoglycan modifications by Streptococcus pneumoniae
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