CAZyme Information: MGYG000000014_02246

Basic Information

• Species: Clostridium butyricum
• Lineage: Bacteria; Firmicutes_A; Clostridia; Clostridiales; Clostridiaceae; Clostridium; Clostridium butyricum
• CAZyme ID: MGYG000000014_02246
• CAZy Family: CE4
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
316	MGYG000000014_8|CGC3	36473.89	9.591

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000000014	4564499	Isolate	United Kingdom	Europe

• Gene Location: Start: 147039; End: 147989 Strand: -

Full Sequence      

MRKRRVNKKKRMILTLVCLIFMGALMCKAWASVDGKVHINKEQTKMEEEQKNKIAEEKSR
QEEEQKRIEAQQRKIEEEKKKSIVGVKAEAEKFSYDAAKVAEKLSKYDYSNDGKKIVFLT
FDDGTSTTVTPEILRILKEENVKATFFLTGQNIERGGDKAKSLIKQEFDDGHAIANHSYS
HDYKILYPNRILNLEAFKQDFNKTDKILKEVLGENFSTRVIRCPGGYMSWKGMGQLDEYL
KEKNMFSIDWNALNGDAEGKRKNAEELKNYAIKTAEGKEMVVILMHDTYGKEETAKSLPG
IIKHFKNNGYEFRTLV

Enzyme Prediction     

EC	3.5.1.41

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	110	236	2.6e-25	0.8384615384615385

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10944	CE4_SmPgdA_like	3.79e-85	115	314	1	189	Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins. This family is represented by a putative polysaccharide deacetylase PgdA from the oral pathogen Streptococcus mutans (SmPgdA) and Bacillus subtilis YheN (BsYheN), which are members of the carbohydrate esterase 4 (CE4) superfamily. SmPgdA is an extracellular metal-dependent polysaccharide deacetylase with a typical CE4 fold, with metal bound to a His-His-Asp triad. It possesses de-N-acetylase activity toward a hexamer of chitooligosaccharide N-acetylglucosamine, but not shorter chitooligosaccharides or a synthetic peptidoglycan tetrasaccharide. SmPgdA plays a role in tuning cell surface properties and in interactions with (salivary) agglutinin, an essential component of the innate immune system, most likely through deacetylation of an as-yet-unidentified polysaccharide. SmPgdA shows significant homology to the catalytic domains of peptidoglycan deacetylases from Streptococcus pneumoniae (SpPgdA) and Listeria monocytogenes (LmPgdA), both of which are involved in the bacterial defense mechanism against human mucosal lysozyme. The Bacillus subtilis genome contains six polysaccharide deacetylase gene homologs: pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH and ylxY. The biological function of BsYheN is still unknown. This family also includes many uncharacterized polysaccharide deacetylases mainly found in bacteria.
cd10917	CE4_NodB_like_6s_7s	3.33e-46	115	306	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.
cd10956	CE4_BH1302_like	6.52e-38	114	314	4	188	Putative catalytic NodB homology domain of uncharacterized BH1302 protein from Bacillus halodurans and its bacterial homologs. This family is represented by a putative polysaccharide deacetylase BH1302 from Bacillus halodurans. Although its biological function is unknown, BH1302 shows high sequence homology to the catalytic NodB homology domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), which is 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. Both BH1302 and SpPgdA belong to the carbohydrate esterase 4 (CE4) superfamily. This family also includes many uncharacterized bacterial polysaccharide deacetylases.
COG0726	CDA1	7.08e-38	111	316	61	254	Peptidoglycan/xylan/chitin deacetylase, PgdA/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis].
cd10948	CE4_BsPdaA_like	7.67e-33	102	315	24	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.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
QGH24331.1	5.42e-206	1	316	1	316
QGH20296.1	5.42e-206	1	316	1	316
QCJ08596.1	1.48e-203	1	316	1	316
AXB86707.1	1.48e-203	1	316	1	316
QJU46226.1	1.48e-203	1	316	1	316

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
2W3Z_A	3.19e-49	89	315	82	310	Structureof a Streptococcus mutans CE4 esterase [Streptococcus mutans UA159]
2C1G_A	3.51e-23	94	315	216	412	Structureof Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) [Streptococcus pneumoniae R6]
5JMU_A	6.37e-23	98	315	3	213	ChainA, Peptidoglycan N-acetylglucosamine deacetylase [[Eubacterium] rectale ATCC 33656]
2C1I_A	1.67e-22	94	315	216	412	Structureof Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) D 275 N Mutant. [Streptococcus pneumoniae R6]
5O6Y_A	9.32e-21	104	315	7	204	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
Q8DP63	2.41e-22	94	315	248	444	Peptidoglycan-N-acetylglucosamine deacetylase OS=Streptococcus pneumoniae (strain ATCC BAA-255 / R6) OX=171101 GN=pgdA PE=1 SV=1
Q81EK9	1.59e-19	104	315	67	264	Peptidoglycan-N-acetylglucosamine deacetylase BC_1960 OS=Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711) OX=226900 GN=BC_1960 PE=1 SV=1
Q81EJ6	2.55e-17	109	312	63	254	Peptidoglycan-N-acetylglucosamine deacetylase BC_1974 OS=Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711) OX=226900 GN=BC_1974 PE=1 SV=1
Q81AF4	4.54e-17	112	315	19	205	Peptidoglycan-N-acetylglucosamine deacetylase BC_3618 OS=Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711) OX=226900 GN=BC_3618 PE=1 SV=1
Q04729	1.52e-16	102	315	51	250	Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1

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
0.006897	0.659381	0.332749	0.000383	0.000296	0.000265

TMHMM  Annotations     

start	end
13	32