CAZyme Information: MGYG000002442_00131

Basic Information

• Species: Gordonibacter sp003339845
• Lineage: Bacteria; Actinobacteriota; Coriobacteriia; Coriobacteriales; Eggerthellaceae; Gordonibacter; Gordonibacter sp003339845
• CAZyme ID: MGYG000002442_00131
• CAZy Family: CE4
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
541	MGYG000002442_1|CGC1	56502.55	7.1245

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000002442	3864912	Isolate	United States	North America

• Gene Location: Start: 142868; End: 144493 Strand: -

Full Sequence      

MHDNYGEHPERSANGGPMPRPDGRARSDDGRGGASGGRRSRESGAFANGNGRSSERGGAA
APGERGAGRPVSYPSSRGGGRPAHSGRIPPQSSGRLPRQGSGRVSQQGRSSRYASTSGAQ
ARPRRANDASSVRSRDAHPAPGQTPYQDRDRYLRISQKPERKGRRLAGVLVSLGVVAAVV
LGAVLFVQSLPANITLNGASVEVHGGKTLADALSASGIKPQPGDLLAVDGSVLEAGKGKP
FHATVNGAVVEDLDKKLASGDVVEIGNGGPIEEPSDAVEQAVPWTVTAEGTGAIHLIEGE
GKDGVKATKTGHLSGITAEQVTQEPSNLARRNVTPNVGDDKVIALTFDDGPWGNQTGEVL
DVLASNGAKATFFTVGDRIERDDGASFVKRAASEGHQVCTHSYDHASGSGQSVNLGYMTP
QEQVAEIEKGYAAIEAATGTEASRIFRAPGGNLGEDVVKNIGPLIKAEIGWNIDSGDWRR
PGPQAIVDELMGAWPGAIVLMHDGGGDRSQTIEALKTALPRLKEQGYRFVTIDELMQYPL
S

Enzyme Prediction     

No EC number prediction in MGYG000002442_00131.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	339	459	1.2e-25	0.8307692307692308

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10917	CE4_NodB_like_6s_7s	4.80e-62	341	523	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.
cd10954	CE4_CtAXE_like	3.88e-58	341	535	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.
TIGR02764	spore_ybaN_pdaB	1.62e-48	339	536	4	191	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]
cd10962	CE4_GT2-like	4.48e-48	341	536	1	195	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.
cd10944	CE4_SmPgdA_like	3.86e-46	341	529	1	187	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.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
QOS70093.1	1.90e-191	181	541	6	365
ACV56945.1	9.98e-184	188	541	2	354
BCS56772.1	7.59e-109	145	538	141	530
BAN76597.1	8.04e-109	145	538	143	532
AHF26020.1	7.74e-108	158	538	33	417

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
7FBW_A	2.49e-30	325	537	101	301	ChainA, Predicted xylanase/chitin deacetylase [Caldanaerobacter subterraneus subsp. tengcongensis MB4]
6HM9_A	6.09e-26	341	536	85	267	Crystalstructure of a BA3943 mutant,a CE4 family pseudoenzyme with restored enzymatic activity. [Bacillus anthracis]
5O6Y_A	1.15e-24	343	537	23	209	Crystalstructure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide [Bacillus cereus ATCC 14579]
6HPA_A	5.73e-24	341	536	86	268	Crystalstructure of a BA3943 mutant,a CE4 family pseudoenzyme [Bacillus anthracis]
2C1G_A	1.27e-23	341	541	236	421	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
Q81AF4	7.32e-35	324	538	8	211	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
P02963	2.87e-28	339	527	19	208	Chitooligosaccharide deacetylase OS=Rhizobium meliloti (strain 1021) OX=266834 GN=nodB PE=3 SV=3
A0A3Q0NBH7	6.11e-28	335	535	260	445	Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serotype 1/2a (strain EGD / Mackaness) OX=1334565 GN=pgdA PE=1 SV=1
Q8Y9V5	6.11e-28	335	535	260	445	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	6.11e-28	335	535	260	445	Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serotype 1/2a (strain 10403S) OX=393133 GN=pgdA PE=2 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
1.000047	0.000001	0.000000	0.000000	0.000000	0.000000

TMHMM  Annotations     

start	end
166	188