CAZyme Information: MGYG000000978_00618

Basic Information

• Species: Streptococcus mitis_D
• Lineage: Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae; Streptococcus; Streptococcus mitis_D
• CAZyme ID: MGYG000000978_00618
• CAZy Family: CE4
• CAZyme Description: Peptidoglycan-N-acetylglucosamine deacetylase

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
463	MGYG000000978_9|CGC1	52812.99	5.5579

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000000978	1233255	MAG	Denmark	Europe

• Gene Location: Start: 31802; End: 33193 Strand: +

Full Sequence      

MDKSRAKRENHDKIRMSLIALVAIFSVSICVLGSIIGYKIYTKQSFEQKIESLKKEKDDQ
LSEGNQKDHFRKGQAEVIAYYPLQREQVISSVQEIMIQDIKENLEDKENLVFYYTEKQDS
TLKGIVNRSVMKQVYDLTSSKVEETEKTSLAKVHLTGDGKPFTLDQLFSDASKAKEQLIK
ELTSFLQDKKLEQEKVDQIVKGLSDQDLSAWNFDYKDSQIILYPSQTVENLDEIALPVSS
FFEVIQSSYLLDKDAELYKAYYEKKNRKVVALTFDDGPNPTTTNQALDTLSKYGIKATFF
VLGKNVSGNEEILKRMKADGHVIGNHSWSHPVLSKLSLDDAKKQITDTEDALTKVLGSSS
KLMRPPYGAITDDIRNSLDLSFIMWDVDSLDWKSKNEASILTEIQREVKNGSIILMHDIH
AETVNALPKVIDYLKGQGYDFVTIPDLLDTRLKAHQLYYNRDQ

Enzyme Prediction     

No EC number prediction in MGYG000000978_00618.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	261	374	7.5e-35	0.8538461538461538

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10947	CE4_SpPgdA_BsYjeA_like	5.91e-101	268	444	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.
cd10954	CE4_CtAXE_like	5.47e-84	268	447	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.
cd10917	CE4_NodB_like_6s_7s	1.24e-80	268	435	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.
pfam18627	PgdA_N	2.81e-80	48	259	1	218	Peptidoglycan GlcNAc deacetylase N-terminal domain. This is the N-terminal and middle domain found in Streptococcus pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA). PgdA protects the Gram-positive bacterial cell wall from host lysozymes by deacetylating peptidoglycan GlcNAc residues. It is a member of the family 4 carbohydrate esterases (CE-4).
cd10962	CE4_GT2-like	1.03e-57	268	449	1	196	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
AYF95397.1	4.17e-314	1	463	1	463
ALD67860.1	5.42e-310	1	463	1	463
QGS42520.1	1.09e-309	1	463	1	463
AMH88872.1	1.09e-309	1	463	1	463
QQQ34807.1	4.45e-309	1	463	1	463

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
2C1G_A	4.25e-252	33	463	1	431	Structureof Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) [Streptococcus pneumoniae R6]
2C1I_A	2.45e-251	33	463	1	431	Structureof Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) D 275 N Mutant. [Streptococcus pneumoniae R6]
6H8L_A	3.97e-58	266	451	8	193	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	3.07e-57	266	451	8	193	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]
5LFZ_A	7.71e-42	268	461	25	218	T48deacetylase [Arthrobacter sp. AW19M34-1],5LGC_A T48 deacetylase with substrate [Arthrobacter sp. AW19M34-1]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q8DP63	3.56e-263	1	463	1	463	Peptidoglycan-N-acetylglucosamine deacetylase OS=Streptococcus pneumoniae (strain ATCC BAA-255 / R6) OX=171101 GN=pgdA PE=1 SV=1
O34798	2.00e-54	266	451	276	461	Peptidoglycan-N-acetylmuramic acid deacetylase PdaC OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaC PE=1 SV=1
Q8Y9V5	2.96e-51	13	461	2	459	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	2.96e-51	13	461	2	459	Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serotype 1/2a (strain 10403S) OX=393133 GN=pgdA PE=2 SV=1
A0A3Q0NBH7	2.96e-51	13	461	2	459	Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serotype 1/2a (strain EGD / Mackaness) OX=1334565 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
0.999997	0.000016	0.000000	0.000000	0.000000	0.000003

TMHMM  Annotations     

start	end
16	38