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CAZyme Information: MGYG000003065_01872

You are here: Home > Sequence: MGYG000003065_01872

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 Ruminococcus_B sp900544395
Lineage Bacteria; Firmicutes_A; Clostridia; Lachnospirales; Lachnospiraceae; Ruminococcus_B; Ruminococcus_B sp900544395
CAZyme ID MGYG000003065_01872
CAZy Family CE4
CAZyme Description Peptidoglycan-N-acetylmuramic acid deacetylase PdaA
CAZyme Property
Protein Length CGC Molecular Weight Isoelectric Point
280 MGYG000003065_28|CGC1 31832.17 5.1739
Genome Property
Genome Assembly ID Genome Size Genome Type Country Continent
MGYG000003065 2628797 MAG United States North America
Gene Location Start: 15141;  End: 15983  Strand: +

Full Sequence      Download help

Enzyme Prediction      help

No EC number prediction in MGYG000003065_01872.

CAZyme Signature Domains help

Family Start End Evalue family coverage
CE4 81 207 5.2e-33 0.9384615384615385

CDD Domains      download full data without filtering help

Cdd ID Domain E-Value qStart qEnd sStart sEnd Domain Description
cd10948 CE4_BsPdaA_like 3.25e-104 52 272 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 1.11e-102 53 275 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]
cd10917 CE4_NodB_like_6s_7s 1.76e-56 88 259 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.
cd10959 CE4_NodB_like_3 1.59e-47 88 272 1 187
Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases. This family includes many uncharacterized bacterial polysaccharide deacetylases. Although their biological function still remains unknown, members in this family show high sequence homology to the catalytic NodB homology domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), which is an extracellular metal-dependent polysaccharide deacetylase with de-N-acetylase activity toward a hexamer of chitooligosaccharide N-acetylglucosamine, but not shorter chitooligosaccharides or a synthetic peptidoglycan tetrasaccharide. Like SpPgdA, this family is a member of the carbohydrate esterase 4 (CE4) superfamily.
COG0726 CDA1 1.42e-44 70 276 47 257
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
QRT31073.1 6.25e-157 1 278 1 278
QEI32529.1 6.25e-157 1 278 1 278
QHB25019.1 6.25e-157 1 278 1 278
CBL24255.1 3.41e-127 25 275 21 270
QUO33551.1 7.71e-126 1 275 1 268

PDB Hits      download full data without filtering help

Hit ID E-Value Query Start Query End Hit Start Hit End Description
1W1A_1 9.57e-65 53 276 24 247
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 1.15e-64 53 276 30 253
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 1.82e-63 53 275 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 5.25e-59 53 278 19 244
Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
6HM9_A 7.41e-31 87 276 84 267
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 3.68e-66 44 276 22 254
Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
O34928 6.29e-64 53 276 30 253
Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
P04675 1.33e-31 88 275 21 218
Chitooligosaccharide deacetylase OS=Bradyrhizobium sp. (strain ANU 289) OX=186901 GN=nodB PE=3 SV=2
P50352 3.69e-31 74 275 7 218
Chitooligosaccharide deacetylase OS=Bradyrhizobium elkanii OX=29448 GN=nodB PE=3 SV=1
P04339 7.21e-30 63 246 9 175
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 OTHER

Other SP_Sec_SPI LIPO_Sec_SPII TAT_Tat_SPI TATLIP_Sec_SPII PILIN_Sec_SPIII
0.643121 0.332051 0.021046 0.000839 0.000597 0.002351

TMHMM  Annotations      download full data without filtering help

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