Any feedback?
Information on EC 3.5.1.104 - peptidoglycan-N-acetylglucosamine deacetylase and Organism(s) Helicobacter pylori and UniProt Accession B5ZA76
for references in articles please use BRENDA:EC3.5.1.104Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
3.5.1.104 peptidoglycan-N-acetylglucosamine deacetylaseIUBMB 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 .
Specify your search results
Word Map
- 3.5.1.104
- lysozyme
-
deacetylation
- streptococcus
- pylori
- helicobacter
- chitin
- cereus
- listeria
- monocytogenes
- anthracis
- muropeptides
-
lysozyme-induced
- chitooligosaccharides
- autolysins
-
de-n-acetylation
-
n-acetylmuramic
- pharmacology
- medicine
The taxonomic range for the selected organisms is: Helicobacter pylori
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
Synonyms
peptidoglycan deacetylase, hp310, sfpgda, peptidoglycan n-acetylglucosamine deacetylase, sppgda, bc1960, glcnac deacetylase, ba1977, bc1974, peptidoglycan glcnac deacetylase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
peptidoglycan 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
75217-01-5
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
peptidoglycan-N-acetyl-D-glucosamine + H2O
peptidoglycan-D-glucosamine + acetate
-
-
-
?
peptidoglycan-N-acetyl-D-glucosamine + H2O
peptidoglycan-D-glucosamine + acetate
the enzyme catalyzes the removal of the acetyl group from the C2 atom of N-acetylglucosamine, which is a constituent of the peptidoglycan found in the cell walls of many bacteria
-
-
?
peptidoglycan-N-acetyl-D-glucosamine + H2O
peptidoglycan-D-glucosamine + acetate
-
-
-
-
?
peptidoglycan-N-acetyl-D-glucosamine + H2O
peptidoglycan-D-glucosamine + acetate
-
-
-
?
peptidoglycan-N-acetyl-D-glucosamine + H2O
peptidoglycan-D-glucosamine + acetate
-
Helicobacter pylori is highly resistant to lysozyme (up to 50 mg/ml), but the HP310 mutant is less resistant compared with the parent strain. The peptidoglycan deacetylation appears to confer lysozyme resistance to escape immunedetection
-
-
?
peptidoglycan-N-acetyl-D-glucosamine + H2O
peptidoglycan-D-glucosamine + acetate
peptidoglycan consists of alternating N-acetylglucosamine and N-acetylmuramic acid residues connected by beta-1,4 bonds and cross-linked via short peptide bridges
-
-
?
additional information
?
-
no substrates: N-acetyl putrescine, N-acetyl spermidine, N-acetyl cadaverine, and N-acetyl dipeptides Ac-D-Ala-D-Ala-OH, Ac-D-Ala-D-Ala-OCH3, Ac-DAla-L-Ala-OH, Ac-D-Ala-L-Ala-OCH3
-
-
?
additional information
?
-
-
no substrates: N-acetyl putrescine, N-acetyl spermidine, N-acetyl cadaverine, and N-acetyl dipeptides Ac-D-Ala-D-Ala-OH, Ac-D-Ala-D-Ala-OCH3, Ac-DAla-L-Ala-OH, Ac-D-Ala-L-Ala-OCH3
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
peptidoglycan-N-acetyl-D-glucosamine + H2O
peptidoglycan-D-glucosamine + acetate
-
-
-
?
peptidoglycan-N-acetyl-D-glucosamine + H2O
peptidoglycan-D-glucosamine + acetate
the enzyme catalyzes the removal of the acetyl group from the C2 atom of N-acetylglucosamine, which is a constituent of the peptidoglycan found in the cell walls of many bacteria
-
-
?
peptidoglycan-N-acetyl-D-glucosamine + H2O
peptidoglycan-D-glucosamine + acetate
-
Helicobacter pylori is highly resistant to lysozyme (up to 50 mg/ml), but the HP310 mutant is less resistant compared with the parent strain. The peptidoglycan deacetylation appears to confer lysozyme resistance to escape immunedetection
-
-
?
peptidoglycan-N-acetyl-D-glucosamine + H2O
peptidoglycan-D-glucosamine + acetate
peptidoglycan consists of alternating N-acetylglucosamine and N-acetylmuramic acid residues connected by beta-1,4 bonds and cross-linked via short peptide bridges
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Zn2+
Fe2+
abolishes the acnB-pgdA transcript binding leading to destabilization of the enzyme's mRNA
additional information
Zn2+
the zinc ion of the metalloenzyme is coordinated by a conserved binding triad of amino acids consisting of one aspartate and two histidine residues, determination of the metal-binding site, which is essential for the enzyme's catalytic activity, one metal site per monomer, structure and quantum chemical calculations of models, overview. The metal ion occupies a tetrahedral environment with binding to one of the carboxylic oxygen of Asp14, His86, His90 and a water molecule
Zn2+
divalent metal binding site, one site per enzyme monomer, essential for the enzyme's catalytic activity, structure analysis, detailed overview
additional information
metal site models show an intrinsic preference for zinc, but also significant flexibility of the site so that binding of other ions can eventually occur, e.g. Fe2+, Co2+, Cu2+, Mg2+, quantum chemical calculations, overview
additional information
-
metal site models show an intrinsic preference for zinc, but also significant flexibility of the site so that binding of other ions can eventually occur, e.g. Fe2+, Co2+, Cu2+, Mg2+, quantum chemical calculations, overview
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
additional information
-
catalytic mechanism possibilities analyzed using the mechanism of reaction of acetyl removal from a model substrate, the N-acetylglucosamine/N-acetylmuramic acid dimer by peptidogylcan deacetylase. Analysis via hybrid quantum chemical/molecular mechanical potential calculations (QC/MM), in conjunction with reaction-path-finding algorithms, molecular docking and molecular dynamics simulations, overview. The active site of this enzyme is in a region of highly negative electrostatic potential and contains a zinc dication with a bound water molecule
physiological function
the enzyme is responsible for a peptidoglycan modification that counteracts the host immune response
physiological function
peptidoglycan deacetylase is the enzyme responsible for a peptidoglycan modification that counteracts the host immune response
physiological function
-
Helicobacter pylori is highly resistant to lysozyme (up to 50 mg/ml), but the HP310 mutant is less resistant compared with the parent strain. The peptidoglycan deacetylation appears to confer lysozyme resistance to escape immunedetection
physiological function
Helicobacter pylori is equipped with a peptidoglycan deacetylase (PgdA) that confers both pure peptidoglycan and whole bacterial resistance to lysozyme degradation, which hydrolyzes the beta-1,4 bonds in peptidoglycan. Under oxidative stress, PgdA is highly expressed and confers resistance to lysozyme in wild-type cells. Role of aconitase (AcnB) in Helicobacter pylori as a posttranscriptional regulator of the cell wall-modifying enzyme peptidoglycan deacetylase PgdA, apo-AcnB directly interacts with the pgdA transcript to enhance stability and increase deacetylase enzyme expression, which impacts in vivo survival
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
tetramer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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, 20°C, 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, 20°C, 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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene hp0310, sequence comparison, recombinant expression of N-terminally His6-tagged enzyme
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
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Wang, G.; Olczak, A.; Forsberg, L.S.; Maier, R.J.
Oxidative stress-induced peptidoglycan deacetylase in Helicobacter pylori
J. Biol. Chem.
284
6790-6800
2009
Helicobacter pylori
Shaik, M.M.; Cendron, L.; Percudani, R.; Zanotti, G.
The structure of Helicobacter pylori HP0310 reveals an atypical peptidoglycan deacetylase
PLoS ONE
6
e19207
2011
Helicobacter pylori (B5ZA76), Helicobacter pylori
Austin, C.M.; Maier, R.J.
Aconitase-mediated posttranscriptional regulation of Helicobacter pylori peptidoglycan deacetylase
J. Bacteriol.
195
5316-5322
2013
Helicobacter pylori (O25080), Helicobacter pylori, Helicobacter pylori ATCC 700392 (O25080)
Munan Shaik, M.; Bhattacharjee, N.; Bhattacharjee, A.; Field, M.; Zanotti, G.
Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations
Proteins
82
1311-1318
2014
Helicobacter pylori (B5ZA76), Helicobacter pylori, Helicobacter pylori G27 (B5ZA76)
EXTERNAL LINKS (specific for EC-Number 3.5.1.104)
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
Release 2023.1 (January 2023)
Legal
Curated at
Member of
