CAZyme Information: MGYG000000404_01211

Basic Information

• Species: UBA11774 sp003507655
• Lineage: Bacteria; Firmicutes_A; Clostridia; Lachnospirales; Lachnospiraceae; UBA11774; UBA11774 sp003507655
• CAZyme ID: MGYG000000404_01211
• CAZy Family: CE4
• CAZyme Description: Peptidoglycan-N-acetylmuramic acid deacetylase PdaA

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
271		30432.72	8.3718

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000000404	2228546	MAG	Sweden	Europe

• Gene Location: Start: 65827; End: 66642 Strand: -

Full Sequence      

MKIKKIRKKKAASVIAAALVLFLAGNGAASLTHQCLSNFSPKKEQVENWGLGFGTEGTQP
SGNATPEELKEYDAHYIGDAKKKVLYLTFDCGYENGNTENIMAALKKHNAPATFFVVGNF
LETSPDLVKKMVKEGYTVGNHTYHHPDMSSISDKASFQKELEGVSNLYKEITGKEMTKYY
RPPQGKYSTENLKMAKELGYQTYFWSLAYVDWNVDAQPTKEEAFNKLLPRVHPGAIVLLH
NTSKTNGEILDELLTKWEEMGYTFKPLSELK

Enzyme Prediction     

No EC number prediction in MGYG000000404_01211.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	77	203	1.5e-33	0.9384615384615385

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10948	CE4_BsPdaA_like	2.13e-108	47	267	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	6.05e-107	48	271	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]
cd10917	CE4_NodB_like_6s_7s	4.76e-57	83	255	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.
TIGR02764	spore_ybaN_pdaB	4.70e-50	78	270	1	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	1.01e-48	65	270	47	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
VCV23051.1	8.10e-140	8	270	24	289
CBL08451.1	1.68e-139	8	270	5	270
CBL11262.1	2.01e-139	8	270	10	275
AEN96348.1	5.10e-133	21	270	18	267
QYX25890.1	6.21e-127	10	270	9	267

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1W1A_1	9.64e-68	48	270	24	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	1.16e-67	48	270	30	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	1.30e-66	48	270	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	8.36e-64	48	270	19	241	Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
6HM9_A	2.04e-32	76	270	78	266	Crystalstructure of a BA3943 mutant,a CE4 family pseudoenzyme with restored enzymatic activity. [Bacillus anthracis]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q04729	8.76e-73	37	270	16	253	Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
O34928	6.35e-67	48	270	30	252	Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
P50850	1.51e-27	76	270	123	311	Uncharacterized protein YlxY OS=Bacillus subtilis (strain 168) OX=224308 GN=ylxY PE=3 SV=2
Q81EK9	9.65e-26	69	270	67	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	2.63e-25	82	270	21	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

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
0.290241	0.534218	0.172409	0.001098	0.000707	0.001307

TMHMM  Annotations     

start	end
13	32