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CAZyme Information: MGYG000003114_00414

You are here: Home > Sequence: MGYG000003114_00414

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 Clostridium sp900547475
Lineage Bacteria; Firmicutes_A; Clostridia; Clostridiales; Clostridiaceae; Clostridium; Clostridium sp900547475
CAZyme ID MGYG000003114_00414
CAZy Family CE4
CAZyme Description Peptidoglycan-N-acetylmuramic acid deacetylase PdaA
CAZyme Property
Protein Length CGC Molecular Weight Isoelectric Point
266 MGYG000003114_3|CGC1 30274.58 5.4083
Genome Property
Genome Assembly ID Genome Size Genome Type Country Continent
MGYG000003114 3467094 MAG United States North America
Gene Location Start: 58562;  End: 59362  Strand: +

Full Sequence      Download help

Enzyme Prediction      help

No EC number prediction in MGYG000003114_00414.

CAZyme Signature Domains help

Family Start End Evalue family coverage
CE4 68 194 5.1e-30 0.9384615384615385

CDD Domains      download full data without filtering help

Cdd ID Domain E-Value qStart qEnd sStart sEnd Domain Description
TIGR02884 spore_pdaA 2.88e-129 39 263 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 2.57e-120 38 259 3 223
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 5.41e-54 75 250 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.
cd10954 CE4_CtAXE_like 3.53e-44 75 262 1 180
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.
cd10950 CE4_BsYlxY_like 3.61e-44 70 262 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.

CAZyme Hits      help

Hit ID E-Value Query Start Query End Hit Start Hit End
AYE35602.1 7.79e-134 1 265 1 262
QAS60989.1 7.79e-134 1 265 1 262
SLK18700.1 1.49e-131 33 264 30 261
QBJ75524.1 1.49e-131 33 264 30 261
ATD57095.1 1.49e-131 33 264 30 261

PDB Hits      download full data without filtering help

Hit ID E-Value Query Start Query End Hit Start Hit End Description
1W1A_1 5.48e-71 23 262 8 246
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]
1W17_A 6.61e-71 23 262 14 252
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]
2J13_A 6.47e-70 39 262 19 241
Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
1NY1_A 2.09e-69 38 262 6 229
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 2.79e-28 61 262 7 207
Crystalstructure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide [Bacillus cereus ATCC 14579]

Swiss-Prot Hits      download full data without filtering help

Hit ID E-Value Query Start Query End Hit Start Hit End Description
O34928 3.62e-70 23 262 14 252
Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
Q04729 3.23e-66 27 262 18 253
Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
Q81AF4 5.41e-28 73 266 20 212
Peptidoglycan-N-acetylglucosamine deacetylase BC_3618 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_3618 PE=1 SV=1
Q81EK9 5.95e-27 61 262 67 267
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
P04339 6.19e-27 61 259 7 215
Chitooligosaccharide deacetylase OS=Rhizobium leguminosarum bv. viciae OX=387 GN=nodB PE=3 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
0.026028 0.972390 0.000568 0.000429 0.000267 0.000260

TMHMM  Annotations      download full data without filtering help

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