Species | Paenibacillus_A phocaensis | |||||||||||
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Lineage | Bacteria; Firmicutes; Bacilli; Paenibacillales; Paenibacillaceae; Paenibacillus_A; Paenibacillus_A phocaensis | |||||||||||
CAZyme ID | MGYG000001535_01341 | |||||||||||
CAZy Family | CE4 | |||||||||||
CAZyme Description | Peptidoglycan-N-acetylmuramic acid deacetylase PdaA | |||||||||||
CAZyme Property |
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Genome Property |
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Gene Location | Start: 251806; End: 252597 Strand: - |
Family | Start | End | Evalue | family coverage |
---|---|---|---|---|
CE4 | 63 | 186 | 2.2e-34 | 0.9230769230769231 |
Cdd ID | Domain | E-Value | qStart | qEnd | sStart | sEnd | Domain Description |
---|---|---|---|---|---|---|---|
TIGR02884 | spore_pdaA | 2.62e-125 | 31 | 255 | 1 | 224 | delta-lactam-biosynthetic de-N-acetylase. Muramic delta-lactam is an unusual constituent of peptidoglycan, found only in bacterial spores in the peptidoglycan wall, or spore cortex. The proteins in this family are PdaA (yfjS), a member of a larger family of polysaccharide deacetylases, and are specificially involved in delta-lactam biosynthesis. PdaA acts immediately after CwlD, an N-acetylmuramoyl-L-alanine amidase and performs a de-N-acetylation. PdaA may also perform the following transpeptidation for lactam ring formation, as heterologous expression in E. coli of CwlD and PdaA together is sufficient for delta-lactam production. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Cellular processes, Sporulation and germination] |
cd10948 | CE4_BsPdaA_like | 1.21e-116 | 28 | 251 | 1 | 223 | Catalytic NodB homology domain of Bacillus subtilis polysaccharide deacetylase PdaA, and its bacterial homologs. The Bacillus subtilis genome contains six polysaccharide deacetylase gene homologs: pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH and ylxY. This family is represented by Bacillus subtilis pdaA gene encoding polysaccharide deacetylase BsPdaA, which is a member of the carbohydrate esterase 4 (CE4) superfamily. BsPdaA deacetylates peptidoglycan N-acetylmuramic acid (MurNAc) residues to facilitate the formation of muramic delta-lactam, which is required for recognition of germination lytic enzymes. BsPdaA deficiency leads to the absence of muramic delta-lactam residues in the spore cortex. Like other CE4 esterases, BsPdaA consists of a single catalytic NodB homology domain that appears to adopt a deformed (beta/alpha)8 barrel fold with a putative substrate binding groove harboring the majority of the conserved residues. It utilizes a general acid/base catalytic mechanism involving a tetrahedral transition intermediate, where a water molecule functions as the nucleophile tightly associated to the zinc cofactor. |
cd10917 | CE4_NodB_like_6s_7s | 1.46e-62 | 68 | 242 | 1 | 171 | Catalytic NodB homology domain of rhizobial NodB-like proteins. This family belongs to the large and functionally diverse carbohydrate esterase 4 (CE4) superfamily, whose members show strong sequence similarity with some variability due to their distinct carbohydrate substrates. It includes many rhizobial NodB chitooligosaccharide N-deacetylase (EC 3.5.1.-)-like proteins, mainly from bacteria and eukaryotes, such as chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan. All members of this family contain a catalytic NodB homology domain with the same overall topology and a deformed (beta/alpha)8 barrel fold with 6- or 7 strands. Their catalytic activity is dependent on the presence of a divalent cation, preferably cobalt or zinc, and they employ a conserved His-His-Asp zinc-binding triad closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. Several family members show diversity both in metal ion specificities and in the residues that coordinate the metal. |
TIGR02764 | spore_ybaN_pdaB | 2.62e-55 | 63 | 254 | 1 | 190 | polysaccharide deacetylase family sporulation protein PdaB. This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterized polysaccharide deacetylase; the exact function this protein family is unknown. [Cellular processes, Sporulation and germination] |
cd10954 | CE4_CtAXE_like | 6.47e-50 | 72 | 254 | 5 | 180 | Catalytic NodB homology domain of Clostridium thermocellum acetylxylan esterase and its bacterial homologs. This family is represented by Clostridium thermocellum acetylxylan esterase (CtAXE, EC 3.1.1.72), a member of the carbohydrate esterase 4 (CE4) superfamily. CtAXE deacetylates O-acetylated xylan, a key component of plant cell walls. It shows no detectable activity on generic esterase substrates including para-nitrophenyl acetate. It is specific for sugar-based substrates and will precipitate acetylxylan, as a consequence of deacetylation. CtAXE is a monomeric protein containing a catalytic NodB homology domain with the same overall topology and a deformed (beta/alpha)8 barrel fold as other CE4 esterases. However, due to differences in the topography of the substrate-binding groove, the chemistry of the active center, and metal ion coordination, CtAXE has different metal ion preference and lacks activity on N-acetyl substrates. It is significantly activated by Co2+. Moreover, CtAXE displays distinctly different ligand coordination to the metal ion, utilizing an aspartate, a histidine, and four water molecules, as opposed to the conserved His-His-Asp zinc-binding triad of other CE4 esterases. |
Hit ID | E-Value | Query Start | Query End | Hit Start | Hit End |
---|---|---|---|---|---|
AZS17709.1 | 3.73e-143 | 1 | 256 | 1 | 261 |
AZK45811.1 | 3.29e-135 | 6 | 254 | 11 | 258 |
QUO43507.1 | 1.25e-130 | 22 | 255 | 25 | 258 |
QQE76429.1 | 1.25e-130 | 22 | 255 | 25 | 258 |
QAV13535.1 | 1.69e-128 | 22 | 254 | 26 | 258 |
Hit ID | E-Value | Query Start | Query End | Hit Start | Hit End | Description |
---|---|---|---|---|---|---|
2J13_A | 6.80e-94 | 24 | 260 | 12 | 247 | Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames] |
1W1A_1 | 8.98e-87 | 10 | 257 | 3 | 249 | Structureof Bacillus subtilis PdaA in complex with NAG, a family 4 Carbohydrate esterase. [Bacillus subtilis],1W1A_2 Structure of Bacillus subtilis PdaA in complex with NAG, a family 4 Carbohydrate esterase. [Bacillus subtilis],1W1B_1 Structure of Bacillus subtilis PdaA with Cadmium, a family 4 Carbohydrate esterase. [Bacillus subtilis],1W1B_2 Structure of Bacillus subtilis PdaA with Cadmium, a family 4 Carbohydrate esterase. [Bacillus subtilis] |
1W17_A | 2.20e-86 | 11 | 257 | 10 | 255 | Structureof Bacillus subtilis PdaA, a family 4 Carbohydrate esterase. [Bacillus subtilis],1W17_B Structure of Bacillus subtilis PdaA, a family 4 Carbohydrate esterase. [Bacillus subtilis] |
1NY1_A | 3.89e-84 | 31 | 257 | 7 | 232 | CrystalStructure Of B. Subtilis Polysaccharide Deacetylase Northeast Structural Genomics Consortium Target Sr127. [Bacillus subtilis],1NY1_B Crystal Structure Of B. Subtilis Polysaccharide Deacetylase Northeast Structural Genomics Consortium Target Sr127. [Bacillus subtilis] |
6HM9_A | 4.79e-31 | 60 | 254 | 77 | 266 | Crystalstructure of a BA3943 mutant,a CE4 family pseudoenzyme with restored enzymatic activity. [Bacillus anthracis] |
Hit ID | E-Value | Query Start | Query End | Hit Start | Hit End | Description |
---|---|---|---|---|---|---|
Q04729 | 1.45e-94 | 5 | 257 | 7 | 256 | Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1 |
O34928 | 1.20e-85 | 11 | 257 | 10 | 255 | Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1 |
Q52845 | 7.89e-33 | 68 | 253 | 21 | 217 | Chitooligosaccharide deacetylase OS=Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099) OX=266835 GN=nodB PE=3 SV=2 |
P02963 | 4.12e-32 | 68 | 240 | 21 | 191 | Chitooligosaccharide deacetylase OS=Rhizobium meliloti (strain 1021) OX=266834 GN=nodB PE=3 SV=3 |
P04675 | 6.09e-32 | 68 | 254 | 21 | 218 | Chitooligosaccharide deacetylase OS=Bradyrhizobium sp. (strain ANU 289) OX=186901 GN=nodB PE=3 SV=2 |
Other | SP_Sec_SPI | LIPO_Sec_SPII | TAT_Tat_SPI | TATLIP_Sec_SPII | PILIN_Sec_SPIII |
---|---|---|---|---|---|
0.000293 | 0.999026 | 0.000176 | 0.000166 | 0.000153 | 0.000142 |
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