CAZyme Information: MGYG000001472_04635

Basic Information

• Species: Oceanobacillus jeddahense
• Lineage: Bacteria; Firmicutes; Bacilli; Bacillales_D; Amphibacillaceae; Oceanobacillus; Oceanobacillus jeddahense
• CAZyme ID: MGYG000001472_04635
• CAZy Family: CE4
• CAZyme Description: Peptidoglycan-N-acetylmuramic acid deacetylase PdaA

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
260	MGYG000001472_7|CGC1	29810.46	4.3765

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000001472	5388095	Isolate	not provided	not provided

• Gene Location: Start: 40246; End: 41028 Strand: -

Full Sequence      

MKTTTTLLLSLAFFLCVFPMNTGYAYGWGYQKNSNHTPPEIGAYQEVLDKYNAFYLDDSG
EKNLYLTFDNGYEQGFTSEILDVLKQEEVPATFFVTGHYVESEPDLVKRMVDEGHIIGNH
SYHHPDFTVMDKEAINKELTDLEQAVAEVSDQDELIYVRPPRGTFSTDTLKWSTELGLVH
VFWSLAFIDWETNSQKGADYAYDEIMKQIHPGAIILLHAVSSDNATALEKVIQDLKQEGY
QFKSLDDLWMSKQLPKQFLY

Enzyme Prediction     

No EC number prediction in MGYG000001472_04635.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	55	179	2.6e-30	0.9307692307692308

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
TIGR02884	spore_pdaA	2.59e-133	27	248	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]
cd10948	CE4_BsPdaA_like	1.74e-122	25	245	2	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	7.75e-61	62	236	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.
TIGR02764	spore_ybaN_pdaB	2.08e-54	58	248	2	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	4.66e-49	53	248	56	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
BAC12836.1	3.41e-140	1	258	1	258
AVQ98268.1	5.42e-126	17	255	17	257
APC47239.1	8.93e-125	1	256	1	258
API91303.1	1.27e-124	9	256	11	259
QTY16977.1	1.27e-124	9	256	11	259

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
2J13_A	1.15e-91	22	253	14	246	Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
1W1A_1	1.85e-90	28	254	25	252	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	2.25e-90	28	254	31	258	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	3.45e-89	28	253	8	234	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]
5O6Y_A	1.50e-34	48	251	7	210	Crystalstructure 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
Q04729	4.75e-102	6	260	10	265	Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
O34928	1.23e-89	28	254	31	258	Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
Q52845	5.06e-37	57	247	16	217	Chitooligosaccharide deacetylase OS=Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099) OX=266835 GN=nodB PE=3 SV=2
P04676	9.92e-36	56	245	12	213	Chitooligosaccharide deacetylase OS=Rhizobium leguminosarum bv. trifolii OX=386 GN=nodB PE=3 SV=1
P50355	1.09e-34	48	245	4	211	Chitooligosaccharide deacetylase OS=Sinorhizobium fredii (strain NBRC 101917 / NGR234) OX=394 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
0.000222	0.999152	0.000153	0.000173	0.000146	0.000136

TMHMM  Annotations     

start	end
7	29