CAZyme Information: MGYG000003595_00374

Basic Information

• Species: HGM11525 sp900770405
• Lineage: Bacteria; Firmicutes_A; Clostridia; Monoglobales_A; UBA1381; HGM11525; HGM11525 sp900770405
• CAZyme ID: MGYG000003595_00374
• CAZy Family: CE4
• CAZyme Description: Peptidoglycan-N-acetylmuramic acid deacetylase PdaA

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
259		28745.32	5.1549

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000003595	2475226	MAG	Fiji	Oceania

• Gene Location: Start: 5740; End: 6519 Strand: +

Full Sequence      

MKKIAAILAGMLLLGGCSAAVQTNSGGYYGIDNTSSGWGFKKEQGKAPDMPEKIRAVLNE
HNAVYIGSQEEKKLYLTFDEGYENGHTTQILDTLAEKKVPAAFFVTGDYFNRSNDLVARM
ISEGHIVGNHTYYHHNLAKLSDPDKIAQELSLLQDKFREQFGCEMKYMRPPEGEYSERVL
AVSADMGYKTVFWSFAYKDWLADDVRGADYAVSQVVPYFHNGAILLLHAVSADNADALGR
IIDSAREQGYEFASLDSLG

Enzyme Prediction     

No EC number prediction in MGYG000003595_00374.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	66	191	8.1e-30	0.9384615384615385

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10948	CE4_BsPdaA_like	5.32e-104	37	255	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.
TIGR02884	spore_pdaA	8.69e-102	37	258	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	3.39e-57	72	246	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.
cd10962	CE4_GT2-like	3.08e-44	72	258	1	194	Catalytic NodB homology domain of uncharacterized bacterial glycosyl transferase, group 2-like family proteins. This family includes many uncharacterized bacterial proteins containing an N-terminal GH18 (glycosyl hydrolase, family 18) domain, a middle NodB-like homology domain, and a C-terminal GT2-like (glycosyl transferase group 2) domain. Although their biological function is unknown, members in this family contain a middle NodB homology domain that is similar to the catalytic domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), 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. The presence of three domains suggests that members of this family may be multifunctional.
COG0726	CDA1	5.27e-44	38	258	30	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
QNO14590.1	7.97e-78	2	258	4	255
ARK29000.1	1.10e-77	32	258	28	255
AIC93790.1	5.02e-77	29	258	23	253
ALX08146.1	6.55e-76	25	258	86	316
ADU74203.1	6.55e-76	25	258	86	316

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
2J13_A	8.90e-71	33	258	15	241	Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
1W17_A	7.47e-60	1	258	1	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]
1W1A_1	2.50e-59	8	258	3	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]
1NY1_A	9.63e-58	31	258	1	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]
2C1G_A	9.28e-27	65	258	229	415	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	1.11e-67	31	258	25	253	Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
O34928	4.09e-59	1	258	1	252	Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
P04339	1.02e-26	56	255	5	215	Chitooligosaccharide deacetylase OS=Rhizobium leguminosarum bv. viciae OX=387 GN=nodB PE=3 SV=1
Q8DP63	6.73e-26	65	258	261	447	Peptidoglycan-N-acetylglucosamine deacetylase OS=Streptococcus pneumoniae (strain ATCC BAA-255 / R6) OX=171101 GN=pgdA PE=1 SV=1
P04675	4.48e-25	72	258	21	218	Chitooligosaccharide deacetylase OS=Bradyrhizobium sp. (strain ANU 289) OX=186901 GN=nodB PE=3 SV=2

SignalP and Lipop Annotations

This protein is predicted as LIPO

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
0.000000	0.000000	1.000045	0.000000	0.000000	0.000000

TMHMM  Annotations     

There is no transmembrane helices in MGYG000003595_00374.