CAZyme Information: MGYG000004458_00288

Basic Information

• Lineage: Bacteria; Firmicutes_A; Clostridia; TANB77; CAG-508; CAG-269
• CAZyme ID: MGYG000004458_00288
• CAZy Family: CE4
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
155	MGYG000004458_3|CGC1	17708.32	8.9183

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000004458	1481528	MAG	Israel	Asia

• Gene Location: Start: 4929; End: 5396 Strand: +

Full Sequence      

MSITKQNKKVKIVNLSILTILIFSLSVICMNNANTKETNSKEISNNKIGWGIKREDNHEQ
PDVGTKNKEVLENNNGICMGNKDKKYIYITFDEGYEAGYTPKILDVLNENNVKGTFFITA
HYLNTQEELVKRMIDEGHIVGNHTPNYLMSRIKKV

Enzyme Prediction     

No EC number prediction in MGYG000004458_00288.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	80	145	7.7e-19	0.49230769230769234

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
TIGR02884	spore_pdaA	3.80e-48	49	144	1	96	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	1.06e-46	48	144	3	99	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.
COG0726	CDA1	1.71e-25	50	144	30	124	Peptidoglycan/xylan/chitin deacetylase, PgdA/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis].
cd10917	CE4_NodB_like_6s_7s	2.93e-25	85	144	1	60	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.
pfam01522	Polysacc_deac_1	7.00e-25	80	144	2	65	Polysaccharide deacetylase. This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase. It also includes chitin deacetylase from yeast, and endoxylanases which hydrolyzes glucosidic bonds in xylan.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
AEG16570.1	8.78e-38	32	147	78	192
ADV79150.1	1.79e-37	35	147	55	167
ABY94197.1	1.79e-37	35	147	55	167
ADH61483.1	1.92e-37	35	147	55	167
ADD03047.1	7.59e-37	35	147	55	167

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1W1A_1	1.15e-35	40	144	15	119	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	1.33e-35	40	144	21	125	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	8.47e-35	43	144	1	102	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	1.24e-32	44	144	14	114	Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
5O6Y_B	3.26e-14	80	144	16	80	Crystalstructure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide [Bacillus cereus ATCC 14579],5O6Y_C Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide [Bacillus cereus ATCC 14579],5O6Y_D Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide [Bacillus cereus ATCC 14579]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
O34928	7.26e-35	40	144	21	125	Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
Q04729	2.13e-34	40	144	22	126	Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
Q52845	9.31e-16	78	147	14	83	Chitooligosaccharide deacetylase OS=Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099) OX=266835 GN=nodB PE=3 SV=2
P02963	9.61e-14	78	144	14	80	Chitooligosaccharide deacetylase OS=Rhizobium meliloti (strain 1021) OX=266834 GN=nodB PE=3 SV=3
P04675	2.68e-13	70	144	9	80	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 OTHER

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
0.659638	0.305320	0.030085	0.000948	0.000644	0.003370

TMHMM  Annotations     

start	end
12	34