CAZyme Information: MGYG000001301_00642

Basic Information

• Species: Parvimonas micra
• Lineage: Bacteria; Firmicutes_A; Clostridia; Tissierellales; Peptoniphilaceae; Parvimonas; Parvimonas micra
• CAZyme ID: MGYG000001301_00642
• CAZy Family: CE4
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
354		40858.29	9.0704

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000001301	1703772	Isolate	not provided	not provided

• Gene Location: Start: 657292; End: 658356 Strand: -

Full Sequence      

MINNEEKNLDDKEKNLDNREKMVDNEEKIKIMRKKRKKNRRKENFIIITAVFLALFIFLG
GKYALDVIYQNKSQVQNKNNQNEQKETSDNNSKEKQSESEKETEQKDSNGIDFAESGNHI
KSADSYAYDTAEIRDYIMSKKEYTGKKMVFLTFDDGVTPGVTDKALDILKEKQVPATFFV
VGKTLNDQAKPYLERQLKEGHGIAIHSFSHDYNKLYPKRVPNPATIKEEAEKTMLRLKEL
LGDKFNTRVWRYPGGHMSWKGLENAGNGDETLKSLGLEWIDWNSLSGDAEPLKVRPTNKE
EMLKYVKTSLSYWKQQNVAVVLMHDSQGKNLTLETLPSIIDYFKSNGYEFGILK

Enzyme Prediction     

No EC number prediction in MGYG000001301_00642.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	142	260	5.3e-24	0.8307692307692308

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10944	CE4_SmPgdA_like	5.18e-69	147	351	1	188	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	4.29e-38	147	344	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.
cd10959	CE4_NodB_like_3	5.41e-30	149	353	3	187	Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases. This family includes many uncharacterized bacterial polysaccharide deacetylases. Although their biological function still remains unknown, members in this family show 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. Like SpPgdA, this family is a member of the carbohydrate esterase 4 (CE4) superfamily.
COG0726	CDA1	2.06e-29	140	350	58	250	Peptidoglycan/xylan/chitin deacetylase, PgdA/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis].
cd10962	CE4_GT2-like	6.80e-27	147	350	1	188	Catalytic NodB homology domain of uncharacterized bacterial glycosyl transferase, group 2-like family proteins. This family includes many uncharacterized bacterial proteins containing an N-terminal GH18 (glycosyl hydrolase, family 18) domain, a middle NodB-like homology domain, and a C-terminal GT2-like (glycosyl transferase group 2) domain. Although their biological function is unknown, members in this family contain a middle NodB homology domain that is similar to the catalytic domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), 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. Like SpPgdA, this family is a member of the carbohydrate esterase 4 (CE4) superfamily. The presence of three domains suggests that members of this family may be multifunctional.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
VEH94616.1	2.04e-220	1	354	1	354
AXU11216.1	1.16e-214	29	354	8	333
AIZ37240.1	7.69e-213	32	354	1	323
QKH80405.1	1.29e-87	115	354	77	319
BAG08597.1	2.08e-86	115	354	77	319

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
2W3Z_A	4.09e-77	118	354	78	311	Structureof a Streptococcus mutans CE4 esterase [Streptococcus mutans UA159]
5JMU_A	8.16e-22	128	350	6	210	ChainA, Peptidoglycan N-acetylglucosamine deacetylase [[Eubacterium] rectale ATCC 33656]
7FBW_A	3.43e-16	137	350	108	293	ChainA, Predicted xylanase/chitin deacetylase [Caldanaerobacter subterraneus subsp. tengcongensis MB4]
2C1G_A	6.29e-16	129	350	222	409	Structureof Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) [Streptococcus pneumoniae R6]
2J13_A	1.40e-15	144	353	52	238	Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
O07596	9.85e-18	138	354	76	274	Putative polysaccharide deacetylase YheN OS=Bacillus subtilis (strain 168) OX=224308 GN=yheN PE=3 SV=1
Q8DP63	3.84e-15	129	350	254	441	Peptidoglycan-N-acetylglucosamine deacetylase OS=Streptococcus pneumoniae (strain ATCC BAA-255 / R6) OX=171101 GN=pgdA PE=1 SV=1
P83513	1.21e-13	146	350	401	577	Bifunctional xylanase/deacetylase OS=Pseudobutyrivibrio xylanivorans OX=185007 GN=xyn11A PE=1 SV=2
Q04729	2.49e-12	146	353	66	250	Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
P24150	2.85e-12	144	220	18	95	Chitooligosaccharide deacetylase OS=Rhizobium leguminosarum bv. phaseoli OX=385 GN=nodB PE=3 SV=1

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
0.999983	0.000044	0.000000	0.000000	0.000000	0.000000

TMHMM  Annotations     

start	end
44	61