CAZyme Information: MGYG000002681_00679

Basic Information

• Species: UMGS1975 sp900546685
• Lineage: Bacteria; Firmicutes_A; Clostridia_A; Christensenellales; QAND01; UMGS1975; UMGS1975 sp900546685
• CAZyme ID: MGYG000002681_00679
• CAZy Family: CE4
• CAZyme Description: Peptidoglycan-N-acetylmuramic acid deacetylase PdaA

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
266	MGYG000002681_27|CGC1	29807.83	5.5796

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000002681	1889419	MAG	Canada	North America

• Gene Location: Start: 6588; End: 7388 Strand: -

Full Sequence      

MKKHEFRRFIDYGILALALALIVQIGLLIPKVTTTMAGGNDWGLSFSEEGAQPRGNADPE
DLAQYDAFFMGSADQKILYLTFDCGYENGNTAAILDTLKSQQVPAAFFVTGHYLEQSPDL
IARMVQEGHIVGNHTYSHPNMSKISTKETLQKELEKNEALYQDITGQPMPKYYRPPAGKY
SIENLQNAKALGYKTMFWSLAYVDWLQDDQPTREQAFDKLLPRTHCGAVILLHNTSSTNA
AILNELIQTWKSQGYSFASLDQLVCP

Enzyme Prediction     

No EC number prediction in MGYG000002681_00679.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	72	196	6.7e-33	0.9230769230769231

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
TIGR02884	spore_pdaA	1.53e-106	41	264	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	4.22e-100	41	260	4	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	1.24e-58	76	251	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.
cd10950	CE4_BsYlxY_like	1.67e-47	93	264	23	188	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.
COG0726	CDA1	6.95e-47	48	263	35	256	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
QUO33551.1	2.74e-108	30	263	36	268
QNM09949.1	1.07e-107	31	263	34	267
QEK18529.1	2.24e-107	35	263	41	268
QCI60928.1	9.79e-107	41	263	38	260
QDW74789.1	1.10e-106	37	264	48	275

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1W1A_1	1.74e-61	41	264	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	2.09e-61	41	264	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	3.35e-60	41	263	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	1.87e-58	40	264	18	242	Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
7FBW_A	6.61e-30	76	264	117	300	ChainA, Predicted xylanase/chitin deacetylase [Caldanaerobacter subterraneus subsp. tengcongensis MB4]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q04729	4.57e-66	42	264	32	254	Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
O34928	1.14e-60	41	264	30	253	Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
Q52845	2.98e-29	75	262	20	217	Chitooligosaccharide deacetylase OS=Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099) OX=266835 GN=nodB PE=3 SV=2
A0A3Q0NBH7	1.38e-28	76	263	266	445	Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serotype 1/2a (strain EGD / Mackaness) OX=1334565 GN=pgdA PE=1 SV=1
Q8Y9V5	1.38e-28	76	263	266	445	Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) OX=169963 GN=pgdA PE=1 SV=1

SignalP and Lipop Annotations

This protein is predicted as OTHER

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
1.000039	0.000000	0.000000	0.000000	0.000000	0.000000

TMHMM  Annotations     

start	end
12	29