CAZyme Information: MGYG000000034_00598

Basic Information

• Species: Massilimaliae timonensis
• Lineage: Bacteria; Firmicutes_A; Clostridia; Oscillospirales; Ruminococcaceae; Massilimaliae; Massilimaliae timonensis
• CAZyme ID: MGYG000000034_00598
• CAZy Family: CE4
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
344		37787.51	4.0885

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000000034	2753532	Isolate	United Kingdom	Europe

• Gene Location: Start: 605803; End: 606837 Strand: -

Full Sequence      

MKKWKFVAMALSLSLLFTACSSSDDDDKNTSSTNSNGVVEDVVSDIGDGTNDVLSDVNDV
VSDVISGTEDVVSDITHGDDDKTDSDLNSGDTTSKTAALPAAGSLENVSVNEAELQALDN
ASHGWGQGKDVDDANRPTSCLTFQEQYGRYAAQFIGDEQKEVYLTFDEGYENGYTAQILD
VLKEKECPAVFFVTMPYVKENPDLIQRMIDEGHVVGNHTVNHPSMPSVSLEQAKQEIAGL
HDYVSENFHYQMTLFRPPRGEWSERTLALTQKLGYDTIFWSFAYQDWEVDAQPDKAMALE
KTVSSVHDGAIYLLHAVSSTNTAILGDFIDQVRAKGYTFATLQA

Enzyme Prediction     

No EC number prediction in MGYG000000034_00598.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	158	277	5.3e-30	0.9

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10948	CE4_BsPdaA_like	4.18e-114	123	342	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	3.37e-97	149	342	25	220	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	5.75e-50	160	333	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.
COG0726	CDA1	4.46e-48	140	342	45	253	Peptidoglycan/xylan/chitin deacetylase, PgdA/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis].
TIGR02764	spore_ybaN_pdaB	6.50e-45	158	342	4	187	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]

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
QNK40789.1	8.22e-101	114	342	65	293
ADU22848.1	9.20e-92	114	337	45	268
AYH41638.1	2.18e-91	92	343	5	255
CCO06017.1	2.04e-87	88	339	29	278
VCV22796.1	2.04e-87	92	339	274	521

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
2J13_A	1.09e-60	117	342	12	238	Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
1W1A_1	2.04e-57	113	342	13	243	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	2.43e-57	113	342	19	249	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	6.01e-55	120	342	3	226	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	9.02e-27	139	342	215	412	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	8.20e-62	117	342	24	250	Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
O34928	1.33e-56	113	342	19	249	Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
Q52845	4.47e-29	156	315	17	174	Chitooligosaccharide deacetylase OS=Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099) OX=266835 GN=nodB PE=3 SV=2
P04339	2.25e-27	156	315	17	174	Chitooligosaccharide deacetylase OS=Rhizobium leguminosarum bv. viciae OX=387 GN=nodB PE=3 SV=1
P02963	2.35e-26	156	315	17	174	Chitooligosaccharide deacetylase OS=Rhizobium meliloti (strain 1021) OX=266834 GN=nodB PE=3 SV=3

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	1.000066	0.000000	0.000000	0.000000

TMHMM  Annotations     

There is no transmembrane helices in MGYG000000034_00598.