CAZyme Information: MGYG000004556_02117

Basic Information

• Lineage: Bacteria; Firmicutes_B; Peptococcia; Peptococcales; Peptococcaceae
• CAZyme ID: MGYG000004556_02117
• CAZy Family: CE4
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
284	MGYG000004556_355|CGC1	31684.62	4.4749

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000004556	3007191	MAG	France	Europe

• Gene Location: Start: 108; End: 962 Strand: +

Full Sequence      

MYSQLLALLLMSGITSAAMPVITPAELPNDPPAITEPYDIPGLQADLAAIAKLDNTSSGW
GPGTRMNKEGRPESPVAYQEKYGQYDADFIKANTENVYLTIDEGYENGYTADILDVLKEK
NCPAVFFVTMPYVKQNPDLVQRMIDEGHVVGSHSVTHPSAGMPSLSLEKQAAEISELHQY
VKEHFDYDMYLFRYPAGIFSEQSLALVQQMGYRSVFWSFAYRDWVTDDQPDPQEALATLA
KRSHPGAIYLLHAVSKTNTQIMGQFIDDTRAAGYTFARYTQDAQ

Enzyme Prediction     

No EC number prediction in MGYG000004556_02117.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	94	214	1.7e-26	0.8923076923076924

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10948	CE4_BsPdaA_like	4.79e-109	59	279	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	1.03e-88	59	277	1	218	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	1.69e-46	97	267	3	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.
COG0726	CDA1	8.12e-40	97	278	67	252	Peptidoglycan/xylan/chitin deacetylase, PgdA/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis].
pfam01522	Polysacc_deac_1	1.75e-34	97	215	9	124	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
VCV22796.1	7.00e-91	50	279	295	524
QNK40789.1	4.07e-88	47	278	63	292
AEN96049.1	2.92e-87	49	276	323	550
BBF42562.1	4.30e-86	15	279	49	314
AYH41638.1	9.56e-75	20	274	4	249

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
2J13_A	6.78e-52	55	276	15	235	Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
1W1A_1	6.05e-46	43	276	8	240	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	7.13e-46	43	276	14	246	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	2.33e-44	53	276	1	223	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]
6HM9_A	3.52e-22	93	281	83	265	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	2.74e-49	51	276	23	247	Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
O34928	3.90e-45	43	276	14	246	Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
P04675	1.67e-21	92	252	18	174	Chitooligosaccharide deacetylase OS=Bradyrhizobium sp. (strain ANU 289) OX=186901 GN=nodB PE=3 SV=2
P04676	8.00e-21	88	252	13	172	Chitooligosaccharide deacetylase OS=Rhizobium leguminosarum bv. trifolii OX=386 GN=nodB PE=3 SV=1
Q52845	1.21e-20	96	252	22	174	Chitooligosaccharide deacetylase OS=Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099) OX=266835 GN=nodB PE=3 SV=2

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
0.000287	0.999121	0.000139	0.000162	0.000134	0.000134

TMHMM  Annotations     

There is no transmembrane helices in MGYG000004556_02117.