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CAZyme Information: MGYG000003412_00369

You are here: Home > Sequence: MGYG000003412_00369

Basic Information | Genomic context | Full Sequence | Enzyme annotations |  CAZy signature domains |  CDD domains | CAZyme hits | PDB hits | Swiss-Prot hits | SignalP and Lipop annotations | TMHMM annotations

Basic Information help

Species HGM12789 sp900766585
Lineage Bacteria; Firmicutes_A; Clostridia; Oscillospirales; Acutalibacteraceae; HGM12789; HGM12789 sp900766585
CAZyme ID MGYG000003412_00369
CAZy Family CE4
CAZyme Description Peptidoglycan-N-acetylmuramic acid deacetylase PdaA
CAZyme Property
Protein Length CGC Molecular Weight Isoelectric Point
271 MGYG000003412_13|CGC1 30186.33 6.7749
Genome Property
Genome Assembly ID Genome Size Genome Type Country Continent
MGYG000003412 2381083 MAG Fiji Oceania
Gene Location Start: 19560;  End: 20375  Strand: -

Full Sequence      Download help

Enzyme Prediction      help

No EC number prediction in MGYG000003412_00369.

CAZyme Signature Domains help

Family Start End Evalue family coverage
CE4 70 197 5.3e-35 0.9461538461538461

CDD Domains      download full data without filtering help

Cdd ID Domain E-Value qStart qEnd sStart sEnd Domain Description
TIGR02884 spore_pdaA 3.01e-112 42 265 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 2.29e-107 42 261 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 5.06e-60 77 250 1 169
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 5.04e-50 72 264 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.
TIGR02764 spore_ybaN_pdaB 3.33e-48 72 264 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]

CAZyme Hits      help

Hit ID E-Value Query Start Query End Hit Start Hit End
BCK85659.1 6.91e-114 27 264 30 267
QCI60928.1 8.54e-114 29 264 25 260
SET81476.1 1.01e-112 41 267 59 285
QRV21970.1 1.14e-112 41 267 32 258
QUO39071.1 2.19e-112 39 270 45 276

PDB Hits      download full data without filtering help

Hit ID E-Value Query Start Query End Hit Start Hit End Description
1W17_A 2.64e-66 15 264 10 252
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]
1W1A_1 3.11e-66 42 264 24 246
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]
1NY1_A 4.19e-65 42 264 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]
2J13_A 6.71e-63 42 264 19 241
Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
6HM9_A 3.43e-28 70 264 78 266
Crystalstructure of a BA3943 mutant,a CE4 family pseudoenzyme with restored enzymatic activity. [Bacillus anthracis]

Swiss-Prot Hits      download full data without filtering help

Hit ID E-Value Query Start Query End Hit Start Hit End Description
Q04729 2.71e-66 42 264 31 253
Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
O34928 1.45e-65 15 264 10 252
Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
P50850 4.01e-28 67 264 120 311
Uncharacterized protein YlxY OS=Bacillus subtilis (strain 168) OX=224308 GN=ylxY PE=3 SV=2
Q52845 1.39e-27 74 263 18 217
Chitooligosaccharide deacetylase OS=Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099) OX=266835 GN=nodB PE=3 SV=2
Q81EK9 9.38e-27 66 264 70 267
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

SignalP and Lipop Annotations help

This protein is predicted as SP

Other SP_Sec_SPI LIPO_Sec_SPII TAT_Tat_SPI TATLIP_Sec_SPII PILIN_Sec_SPIII
0.010129 0.988641 0.000482 0.000274 0.000217 0.000225

TMHMM  Annotations      download full data without filtering help

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