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CAZyme Information: MGYG000001472_04635

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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 Oceanobacillus jeddahense
Lineage Bacteria; Firmicutes; Bacilli; Bacillales_D; Amphibacillaceae; Oceanobacillus; Oceanobacillus jeddahense
CAZyme ID MGYG000001472_04635
CAZy Family CE4
CAZyme Description Peptidoglycan-N-acetylmuramic acid deacetylase PdaA
CAZyme Property
Protein Length CGC Molecular Weight Isoelectric Point
260 MGYG000001472_7|CGC1 29810.46 4.3765
Genome Property
Genome Assembly ID Genome Size Genome Type Country Continent
MGYG000001472 5388095 Isolate not provided not provided
Gene Location Start: 40246;  End: 41028  Strand: -

Full Sequence      Download help

Enzyme Prediction      help

No EC number prediction in MGYG000001472_04635.

CAZyme Signature Domains help

Family Start End Evalue family coverage
CE4 55 179 2.6e-30 0.9307692307692308

CDD Domains      download full data without filtering help

Cdd ID Domain E-Value qStart qEnd sStart sEnd Domain Description
TIGR02884 spore_pdaA 2.59e-133 27 248 1 223
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]
cd10948 CE4_BsPdaA_like 1.74e-122 25 245 2 223
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 7.75e-61 62 236 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, bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC, 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 2.08e-54 58 248 2 190
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]
COG0726 CDA1 4.66e-49 53 248 56 256
Peptidoglycan/xylan/chitin deacetylase, PgdA/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis].

CAZyme Hits      help

Hit ID E-Value Query Start Query End Hit Start Hit End
BAC12836.1 3.41e-140 1 258 1 258
AVQ98268.1 5.42e-126 17 255 17 257
APC47239.1 8.93e-125 1 256 1 258
API91303.1 1.27e-124 9 256 11 259
QTY16977.1 1.27e-124 9 256 11 259

PDB Hits      download full data without filtering help

Hit ID E-Value Query Start Query End Hit Start Hit End Description
2J13_A 1.15e-91 22 253 14 246
Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
1W1A_1 1.85e-90 28 254 25 252
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 2.25e-90 28 254 31 258
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 3.45e-89 28 253 8 234
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 1.50e-34 48 251 7 210
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 4.75e-102 6 260 10 265
Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
O34928 1.23e-89 28 254 31 258
Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
Q52845 5.06e-37 57 247 16 217
Chitooligosaccharide deacetylase OS=Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099) OX=266835 GN=nodB PE=3 SV=2
P04676 9.92e-36 56 245 12 213
Chitooligosaccharide deacetylase OS=Rhizobium leguminosarum bv. trifolii OX=386 GN=nodB PE=3 SV=1
P50355 1.09e-34 48 245 4 211
Chitooligosaccharide deacetylase OS=Sinorhizobium fredii (strain NBRC 101917 / NGR234) OX=394 GN=nodB PE=3 SV=2

SignalP and Lipop Annotations help

This protein is predicted as SP

0.000222 0.999152 0.000153 0.000173 0.000146 0.000136

TMHMM  Annotations      download full data without filtering help

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