Species | UMGS856 sp900546265 | |||||||||||
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Lineage | Bacteria; Firmicutes_A; Clostridia; Oscillospirales; Acutalibacteraceae; UMGS856; UMGS856 sp900546265 | |||||||||||
CAZyme ID | MGYG000002711_01292 | |||||||||||
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: 91496; End: 92299 Strand: - |
Family | Start | End | Evalue | family coverage |
---|---|---|---|---|
CE4 | 72 | 198 | 2.7e-36 | 0.9384615384615385 |
Cdd ID | Domain | E-Value | qStart | qEnd | sStart | sEnd | Domain Description |
---|---|---|---|---|---|---|---|
TIGR02884 | spore_pdaA | 1.84e-116 | 44 | 267 | 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 | 2.26e-113 | 44 | 263 | 4 | 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 | 8.25e-63 | 79 | 250 | 1 | 167 | 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. |
cd10950 | CE4_BsYlxY_like | 2.50e-53 | 74 | 266 | 1 | 187 | Putative catalytic NodB homology domain of uncharacterized protein YlxY from Bacillus subtilis 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 putative polysaccharide deacetylase BsYlxY, encoded by the ylxY gene, which is a member of the carbohydrate esterase 4 (CE4) superfamily. Although its biological function still remains unknown, BsYlxY shows high sequence homology to the catalytic domain of Bacillus subtilis pdaB gene encoding a putative polysaccharide deacetylase (BsPdaB), which is essential for the maintenance of spores after the late stage of sporulation and is highly conserved in spore-forming bacteria. However, disruption of the ylxY gene in B. subtilis did not cause any sporulation defect. Moreover, the Asp residue in the classical His-His-Asp zinc-binding motif of CE4 esterases is mutated to a Val residue in this family. Other catalytically relevant residues of CE4 esterases are also not conserved, which suggest that members of this family may be inactive. |
COG0726 | CDA1 | 1.53e-50 | 61 | 266 | 47 | 256 | Peptidoglycan/xylan/chitin deacetylase, PgdA/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis]. |
Hit ID | E-Value | Query Start | Query End | Hit Start | Hit End |
---|---|---|---|---|---|
BCI60049.1 | 9.18e-139 | 1 | 266 | 1 | 265 |
QNO19102.1 | 9.97e-131 | 1 | 266 | 9 | 274 |
QIX92898.1 | 1.83e-129 | 31 | 267 | 39 | 273 |
ASN94259.1 | 2.59e-129 | 31 | 266 | 39 | 272 |
QRP41062.1 | 2.59e-129 | 31 | 266 | 39 | 272 |
Hit ID | E-Value | Query Start | Query End | Hit Start | Hit End | Description |
---|---|---|---|---|---|---|
1W1A_1 | 2.48e-72 | 24 | 266 | 2 | 246 | 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] |
2J13_A | 1.67e-70 | 44 | 266 | 19 | 241 | Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames] |
1W17_A | 1.94e-70 | 8 | 266 | 2 | 252 | 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 | 4.33e-69 | 44 | 266 | 7 | 229 | 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] |
5O6Y_A | 3.52e-38 | 64 | 266 | 6 | 207 | Crystalstructure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide [Bacillus cereus ATCC 14579] |
Hit ID | E-Value | Query Start | Query End | Hit Start | Hit End | Description |
---|---|---|---|---|---|---|
Q04729 | 2.75e-78 | 36 | 266 | 19 | 253 | Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1 |
O34928 | 1.06e-69 | 8 | 266 | 2 | 252 | Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1 |
Q81EK9 | 4.72e-37 | 32 | 266 | 34 | 267 | Peptidoglycan-N-acetylglucosamine deacetylase BC_1960 OS=Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711) OX=226900 GN=BC_1960 PE=1 SV=1 |
A0A3Q0NBH7 | 8.65e-33 | 77 | 266 | 264 | 445 | Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serotype 1/2a (strain EGD / Mackaness) OX=1334565 GN=pgdA PE=1 SV=1 |
Q8Y9V5 | 8.65e-33 | 77 | 266 | 264 | 445 | Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) OX=169963 GN=pgdA PE=1 SV=1 |
Other | SP_Sec_SPI | LIPO_Sec_SPII | TAT_Tat_SPI | TATLIP_Sec_SPII | PILIN_Sec_SPIII |
---|---|---|---|---|---|
0.001190 | 0.997908 | 0.000264 | 0.000269 | 0.000181 | 0.000157 |
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