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CAZyme Information: MGYG000002047_00488

You are here: Home > Sequence: MGYG000002047_00488

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 UMGS902 sp003343845
Lineage Bacteria; Firmicutes_A; Clostridia; Oscillospirales; CAG-272; UMGS902; UMGS902 sp003343845
CAZyme ID MGYG000002047_00488
CAZy Family CE4
CAZyme Description Peptidoglycan-N-acetylmuramic acid deacetylase PdaA
CAZyme Property
Protein Length CGC Molecular Weight Isoelectric Point
258 29571.8 6.3042
Genome Property
Genome Assembly ID Genome Size Genome Type Country Continent
MGYG000002047 2115875 MAG China Asia
Gene Location Start: 34024;  End: 34800  Strand: +

Full Sequence      Download help

Enzyme Prediction      help

No EC number prediction in MGYG000002047_00488.

CAZyme Signature Domains help

Family Start End Evalue family coverage
CE4 65 190 2.9e-27 0.9307692307692308

CDD Domains      download full data without filtering help

Cdd ID Domain E-Value qStart qEnd sStart sEnd Domain Description
cd10948 CE4_BsPdaA_like 1.25e-98 30 255 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.
TIGR02884 spore_pdaA 1.19e-95 32 258 2 223
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]
cd10917 CE4_NodB_like_6s_7s 1.87e-50 71 243 1 168
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.
COG0726 CDA1 7.33e-41 62 258 56 256
Peptidoglycan/xylan/chitin deacetylase, PgdA/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis].
cd10954 CE4_CtAXE_like 1.10e-37 71 258 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.

CAZyme Hits      help

Hit ID E-Value Query Start Query End Hit Start Hit End
CED94346.1 7.83e-83 25 258 44 272
CEK37806.1 5.97e-82 25 258 43 271
AUN13963.1 5.97e-82 25 258 43 271
CEJ73318.1 5.97e-82 25 258 43 271
QYE99241.1 5.97e-82 25 258 43 271

PDB Hits      download full data without filtering help

Hit ID E-Value Query Start Query End Hit Start Hit End Description
2J13_A 4.15e-55 67 258 51 241
Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
1W1A_1 1.40e-49 28 258 21 246
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 1.66e-49 28 258 27 252
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 1.93e-48 28 258 4 229
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 3.63e-26 73 258 23 207
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
Q04729 6.71e-58 7 258 7 253
Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
O34928 9.07e-49 28 258 27 252
Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
Q81EK9 7.26e-25 73 258 83 267
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
Q81AF4 1.10e-23 68 258 19 208
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
A0A3Q0NBH7 3.75e-23 70 258 265 445
Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serotype 1/2a (strain EGD / Mackaness) OX=1334565 GN=pgdA 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
0.000241 0.999120 0.000180 0.000147 0.000143 0.000140

TMHMM  Annotations      download full data without filtering help

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