CAZyme Information: MGYG000001395_01019

Basic Information

• Species: Listeria innocua
• Lineage: Bacteria; Firmicutes; Bacilli; Lactobacillales; Listeriaceae; Listeria; Listeria innocua
• CAZyme ID: MGYG000001395_01019
• CAZy Family: CE4
• CAZyme Description: Peptidoglycan-N-acetylmuramic acid deacetylase PdaC

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
466	MGYG000001395_14|CGC7	52355.57	9.9528

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000001395	2890785	Isolate	not provided	not provided

• Gene Location: Start: 184699; End: 186099 Strand: +

Full Sequence      

MKIRWIKVSLVTILIIAVVFVGVIGFQKYQFSKSRNKVIMQMDRLMKDQDGGNFRRLDKK
EDGVEIISYIPKTSTKQDNEIIQKEIEKAKSAEIKKLNRDKDKQGIIFYTYQKQKMAEQV
VSYKAVQSEYVKEGKTKFVLKDKKDICKNIVTDAKTGALLTLGDVLIKNDETKLNLKTAA
EQELVKTGDIPLKDVGKLGGIKSLVKWDQTDFELTNSELIVPVEAPGISGPKKVNLKLAD
IASSVNKRYLPSSVKVPEIPKAKTNKRIALTFDDGPSASVTPGVLDTLKRYDVKATFFVL
GSSVVQNPGLVKRELDEGHQVGSHSWDHPQLTKLSEQEVYNQILQTQKVVFDQTGYFPTT
MRPPYGAVNKKVADEIGLPIIQWSVDTEDWKNKNAKVVTQRVLAGATDGAIVLMHDIHKT
TAASLDETLKQLKSQGFEFVTINELYGEKLQIGKQYFDKTESRMVK

Enzyme Prediction     

No EC number prediction in MGYG000001395_01019.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	263	374	1.9e-32	0.8615384615384616

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10954	CE4_CtAXE_like	8.08e-83	266	445	1	180	Catalytic NodB homology domain of Clostridium thermocellum acetylxylan esterase and its bacterial homologs. This family is represented by Clostridium thermocellum acetylxylan esterase (CtAXE, EC 3.1.1.72), a member of the carbohydrate esterase 4 (CE4) superfamily. CtAXE deacetylates O-acetylated xylan, a key component of plant cell walls. It shows no detectable activity on generic esterase substrates including para-nitrophenyl acetate. It is specific for sugar-based substrates and will precipitate acetylxylan, as a consequence of deacetylation. CtAXE is a monomeric protein containing a catalytic NodB homology domain with the same overall topology and a deformed (beta/alpha)8 barrel fold as other CE4 esterases. However, due to differences in the topography of the substrate-binding groove, the chemistry of the active center, and metal ion coordination, CtAXE has different metal ion preference and lacks activity on N-acetyl substrates. It is significantly activated by Co2+. Moreover, CtAXE displays distinctly different ligand coordination to the metal ion, utilizing an aspartate, a histidine, and four water molecules, as opposed to the conserved His-His-Asp zinc-binding triad of other CE4 esterases.
cd10947	CE4_SpPgdA_BsYjeA_like	4.21e-81	266	442	1	177	Catalytic NodB homology domain of Streptococcus pneumoniae peptidoglycan deacetylase PgdA, Bacillus subtilis BsYjeA protein, and their bacterial homologs. This family is represented by Streptococcus pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA), a member of the carbohydrate esterase 4 (CE4) superfamily. SpPgdA protects gram-positive bacterial cell wall from host lysozymes by deacetylating peptidoglycan N-acetylglucosamine (GlcNAc) residues. It consists of three separate domains: N-terminal, middle and C-terminal (catalytic) domains. The catalytic NodB homology domain is similar to the deformed (beta/alpha)8 barrel fold adopted by other CE4 esterases, which harbors a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad closely associated with conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The enzyme is able to accept GlcNAc3 as a substrate, with the N-acetyl of the middle sugar being removed by the enzyme. This family also includes Bacillus subtilis BsYjeA protein encoded by the yjeA gene, which is one of the six polysaccharide deacetylase gene homologs (pdaA, pdaB/ybaN, yheN, yjeA, yxkH and ylxY) in the Bacillus subtilis genome. Although homology comparison shows that the BsYjeA protein contains a polysaccharide deacetylase domain, and was predicted to be a membrane-bound xylanase or a membrane-bound chitooligosaccharide deacetylase, more recent research indicates BsYjeA might be a novel non-specific secretory endonuclease which creates random nicks progressively on the two strands of dsDNA, resulting in highly distinguishable intermediates/products very different in chemical and physical compositions over time. In addition, BsYjeA shares several enzymatic properties with the well-understood DNase I endonuclease. Both enzymes are active on ssDNA and dsDNA, both generate random nicks, and both require Mg2+ or Mn2+ for hydrolytic activity.
cd10917	CE4_NodB_like_6s_7s	1.17e-79	266	433	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	1.17e-56	257	449	56	260	Peptidoglycan/xylan/chitin deacetylase, PgdA/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis].
cd10959	CE4_NodB_like_3	1.62e-56	266	441	1	186	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.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
CAC95669.1	0.0	1	466	1	466
QUR86291.1	0.0	1	466	1	466
QGF42558.1	0.0	1	466	1	466
QOF62758.1	1.96e-309	1	466	1	466
AKS53026.1	6.54e-308	1	466	1	466

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
6H8L_A	5.44e-55	266	451	10	195	Structureof peptidoglycan deacetylase PdaC from Bacillus subtilis [Bacillus subtilis subsp. subtilis str. 168],6H8L_B Structure of peptidoglycan deacetylase PdaC from Bacillus subtilis [Bacillus subtilis subsp. subtilis str. 168]
6H8N_A	4.18e-54	266	451	10	195	Structureof peptidoglycan deacetylase PdaC from Bacillus subtilis - mutant D285S [Bacillus subtilis subsp. subtilis str. 168],6H8N_B Structure of peptidoglycan deacetylase PdaC from Bacillus subtilis - mutant D285S [Bacillus subtilis subsp. subtilis str. 168]
2C1G_A	1.89e-53	211	461	180	431	Structureof Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) [Streptococcus pneumoniae R6]
2C1I_A	1.00e-52	211	461	180	431	Structureof Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) D 275 N Mutant. [Streptococcus pneumoniae R6]
7FBW_A	1.16e-46	264	445	115	299	ChainA, Predicted xylanase/chitin deacetylase [Caldanaerobacter subterraneus subsp. tengcongensis MB4]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
A0A3Q0NBH7	4.12e-289	1	466	1	466	Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serotype 1/2a (strain EGD / Mackaness) OX=1334565 GN=pgdA PE=1 SV=1
Q8Y9V5	4.12e-289	1	466	1	466	Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) OX=169963 GN=pgdA PE=1 SV=1
A0A0H3GDH9	4.12e-289	1	466	1	466	Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serotype 1/2a (strain 10403S) OX=393133 GN=pgdA PE=2 SV=1
O34798	5.67e-55	166	451	171	463	Peptidoglycan-N-acetylmuramic acid deacetylase PdaC OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaC PE=1 SV=1
Q8DP63	7.71e-53	2	461	13	463	Peptidoglycan-N-acetylglucosamine deacetylase OS=Streptococcus pneumoniae (strain ATCC BAA-255 / R6) OX=171101 GN=pgdA PE=1 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
0.938844	0.022282	0.007320	0.000196	0.000105	0.031286

TMHMM  Annotations     

start	end
5	27