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Information on EC 3.5.1.104 - peptidoglycan-N-acetylglucosamine deacetylase and Organism(s) Streptococcus pneumoniae and UniProt Accession Q8DP63

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IUBMB Comments
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 .
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Streptococcus pneumoniae
UNIPROT: Q8DP63
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The taxonomic range for the selected organisms is: Streptococcus pneumoniae
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
peptidoglycan deacetylase, hp310, sfpgda, peptidoglycan n-acetylglucosamine deacetylase, sppgda, bc1960, glcnac deacetylase, bc1974, ba1977, bc3618, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
peptidoglycan GlcNAc deacetylase
-
N-acetylglucosamine deacetylase
-
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
-
SUBSTRATE
PRODUCT                       
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
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc + H2O
GlcNAc-beta-1,4-GlcN-beta-1,4-GlcNAc + acetate
show the reaction diagram
-
-
-
?
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
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 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
-
-
-
-
?
additional information
?
-
-
enzyme is inactive against peptidoglycans from Staphylococcus aureus, Staphylococcus carnosus or Escherichia coli. No substrate: N-acetylglucosamine
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
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 GlcNAc deacetylase protects the Gram-positive bacterial cell wall from host lysozymes by deacetylating peptidoglycan GlcNAc residues
-
-
?
acetylated peptidoglycan + H2O
deacetylated peptidoglycan + acetate
show the reaction diagram
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
0.05 mM, 30fold increase in activity
Zn2+
0.05 mM, 5.5fold increase in activity
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-[[4-(diethylamino)-2-hydroxyphenyl]carbonyl]benzoic acid
-
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
-
1 mM, 29% residual activity
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3.8 - 26
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc
16.7
4-nitrophenyl acetate
-
37°C, pH 7.0
2.27 - 2.38
4-yethylumbelliferyl acetate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.27 - 1.6
GlcNAc-beta-1,4-GlcNAc-beta-1,4-GlcNAc
0.46
4-nitrophenyl acetate
-
37°C, pH 7.0
0.28 - 1.64
4-yethylumbelliferyl acetate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0288
4-nitrophenyl acetate
-
37°C, pH 7.0
0.129 - 0.71
4-yethylumbelliferyl acetate
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.13
2-[[4-(diethylamino)-2-hydroxyphenyl]carbonyl]benzoic acid
Streptococcus pneumoniae
-
37°C, 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
-
37°C, pH 7.0
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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)
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
peptidoglycan modifications during colonizing the mucosal surface of the upper respiratory tract, lysozyme M-sufficient mice
Manually annotated by BRENDA team
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
sitting-drop vapor diffusion method, native crystal structure and product complexes of SpPgdA
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
generation of mutant (pgdA and pgdAadr) and revertant strains
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pharmacology
studies on peptidoglycan modifications by Streptococcus pneumoniae
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Blair, D.E.; Schuttelkopf, A.W.; MacRae, J.I.; van Aalten, D.M.F.
Structure and metal-dependent mechanism of peptidoglycan deacetylase, a streptococcal virulence factor
Proc. Natl. Acad. Sci. USA
102
15429-15434
2005
Streptococcus pneumoniae (Q8DP63), Streptococcus pneumoniae
Manually annotated by BRENDA team
Davis, K.M.; Akinbi, H.T.; Standish, A.J.; Weiser, J.N.
Resistance to mucosal lysozyme compensates for the fitness deficit of peptidoglycan modifications by Streptococcus pneumoniae
PLoS Pathog.
4
e1000241
2008
Streptococcus pneumoniae (A0A0H2UQQ3)
Manually annotated by BRENDA team
Bui, N.K.; Turk, S.; Buckenmaier, S.; Stevenson-Jones, F.; Zeuch, B.; Gobec, S.; Vollmer, W.
Development of screening assays and discovery of initial inhibitors of pneumococcal peptidoglycan deacetylase PgdA
Biochem. Pharmacol.
82
43-52
2011
Streptococcus pneumoniae
Manually annotated by BRENDA team