CAZyme Information: MGYG000000375_00961

Basic Information

• Lineage: Bacteria; Firmicutes_A; Clostridia; TANB77; CAG-508; CAG-269
• CAZyme ID: MGYG000000375_00961
• CAZy Family: CE4
• CAZyme Description: Peptidoglycan-N-acetylmuramic acid deacetylase PdaA

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
266	MGYG000000375_8|CGC1	30900.11	6.1106

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000000375	1473545	MAG	Sweden	Europe

• Gene Location: Start: 53327; End: 54127 Strand: +

Full Sequence      

MKNNMIKKISMTLLIVIVSIFTILDMSNERAIKTNSQLNNKKIGWGIKRNDNHDQPDVGE
ENKKVLEENNGICLGNKDKKVIYLTFDEGYEAGYTEKILTTLRENNVKATFFITAHYLNT
QEELVKKMIDEGHILGNHTVNHKSMPDLTEEEIKKEVMDLHESIYKKFGYEMKYIRPPKG
EFSEKTLNVTNSLGYKNVMWSFGYEDWNENKQPDENSAIKKITNNFHNGEIMLLHGNSKT
NTNILDSVIKEAKNMEYEFKSLDEFE

Enzyme Prediction     

No EC number prediction in MGYG000000375_00961.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	76	197	5.8e-30	0.9153846153846154

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10948	CE4_BsPdaA_like	1.02e-104	41	262	1	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	3.68e-98	44	264	1	222	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	2.35e-54	80	253	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.
TIGR02764	spore_ybaN_pdaB	2.37e-48	75	264	1	189	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	8.65e-48	62	266	47	257	Peptidoglycan/xylan/chitin deacetylase, PgdA/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis].

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
AEG16570.1	1.94e-79	28	264	78	313
ALX08146.1	3.69e-77	31	264	82	315
ADU74203.1	3.69e-77	31	264	82	315
ABN52306.1	3.69e-77	31	264	82	315
ANV75893.1	3.69e-77	31	264	82	315

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
2J13_A	1.61e-62	40	264	15	240	Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
1W1A_1	8.72e-62	40	264	20	245	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	1.04e-61	40	264	26	251	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	8.35e-61	40	264	3	228	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]
2C1G_A	1.30e-30	77	264	233	414	Structureof Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) [Streptococcus pneumoniae R6]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q04729	1.14e-66	34	264	21	252	Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
O34928	5.72e-61	40	264	26	251	Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
Q8DP63	1.02e-29	77	264	265	446	Peptidoglycan-N-acetylglucosamine deacetylase OS=Streptococcus pneumoniae (strain ATCC BAA-255 / R6) OX=171101 GN=pgdA PE=1 SV=1
Q81EK9	1.56e-27	75	262	76	264	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	4.11e-27	78	264	20	207	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

SignalP and Lipop Annotations

This protein is predicted as SP

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
0.148026	0.798674	0.051855	0.000456	0.000406	0.000549

TMHMM  Annotations     

start	end
9	26