CAZyme Information: MGYG000001460_01997

Basic Information

• Species: Romboutsia dakarensis
• Lineage: Bacteria; Firmicutes_A; Clostridia; Peptostreptococcales; Peptostreptococcaceae; Romboutsia; Romboutsia dakarensis
• CAZyme ID: MGYG000001460_01997
• CAZy Family: CE4
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
269	MGYG000001460_113|CGC1	30919.97	7.4467

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000001460	3735762	Isolate	not provided	not provided

• Gene Location: Start: 12753; End: 13562 Strand: -

Full Sequence      

MEAKNKGKIIIFLSTGVLTLGIISSNIKIGYGYTKNHKDFRNENLSDTTITEIIYNTTQE
VNKGPMKSSGKVAYITIDDGPSKYTDRIIEILDKYNAKGTFFMIDRNMKSYPEQVKNIVE
SGNTAGFHSVSHDIHKLYKKNISAKEEFDINRKTFYDITGQESSLVRLPYGSKPYTPSES
YKALVDANYKVWDWNVDTEDWKSDSNKILENVKMYSKNEDDIVVLIHEKKQTVESLDKVL
KYLSEQGYELLPISQSQDPKNFWIGNLYK

Enzyme Prediction     

No EC number prediction in MGYG000001460_01997.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	68	192	9.7e-24	0.9153846153846154

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10944	CE4_SmPgdA_like	3.08e-72	71	252	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	2.63e-40	71	243	1	170	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	2.50e-38	71	255	1	179	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	2.55e-36	71	253	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.
cd10962	CE4_GT2-like	2.58e-34	74	254	4	192	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
AXU49803.1	9.22e-116	5	267	9	276
AXU64235.1	9.22e-116	5	267	9	276
AXU31379.1	9.22e-116	5	267	9	276
AXU27581.1	9.22e-116	5	267	9	276
AXU35167.1	9.22e-116	5	267	9	276

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
5NC6_A	1.38e-35	71	266	1	203	Crystalstructure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (E)-N-hydroxy-3-(naphthalen-1-yl)prop-2-enamide [Bacillus cereus]
5N1J_A	1.42e-35	71	266	2	204	Crystalstructure of the polysaccharide deacetylase Bc1974 from Bacillus cereus [Bacillus cereus],5N1J_B Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus [Bacillus cereus],5N1J_C Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus [Bacillus cereus],5N1J_D Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus [Bacillus cereus],5N1P_A Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with N-hydroxynaphthalene-1-carboxamide [Bacillus cereus],5N1P_B Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with N-hydroxynaphthalene-1-carboxamide [Bacillus cereus],5N1P_C Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with N-hydroxynaphthalene-1-carboxamide [Bacillus cereus],5N1P_D Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with N-hydroxynaphthalene-1-carboxamide [Bacillus cereus]
5NC9_A	1.49e-35	60	266	28	245	Crystalstructure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (2S)-2,6-diamino-N-hydroxyhexanamide [Bacillus cereus ATCC 14579],5NC9_B Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (2S)-2,6-diamino-N-hydroxyhexanamide [Bacillus cereus ATCC 14579],5NC9_C Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (2S)-2,6-diamino-N-hydroxyhexanamide [Bacillus cereus ATCC 14579],5NC9_D Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (2S)-2,6-diamino-N-hydroxyhexanamide [Bacillus cereus ATCC 14579],5NCD_A Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (2S)-2-amino-5-(diaminomethylideneamino)-N-hydroxypentanamide [Bacillus cereus],5NCD_B Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (2S)-2-amino-5-(diaminomethylideneamino)-N-hydroxypentanamide [Bacillus cereus],5NCD_C Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (2S)-2-amino-5-(diaminomethylideneamino)-N-hydroxypentanamide [Bacillus cereus],5NCD_D Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (2S)-2-amino-5-(diaminomethylideneamino)-N-hydroxypentanamide [Bacillus cereus],5NEK_A Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with acetazolamide [Bacillus cereus],5NEK_B Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with acetazolamide [Bacillus cereus],5NEK_C Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with acetazolamide [Bacillus cereus],5NEK_D Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with acetazolamide [Bacillus cereus],5NEL_A Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with ThiametG [Bacillus cereus],5NEL_B Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with ThiametG [Bacillus cereus],5NEL_C Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with ThiametG [Bacillus cereus],5NEL_D Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with ThiametG [Bacillus cereus]
5NC6_B	2.80e-35	60	266	54	271	Crystalstructure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (E)-N-hydroxy-3-(naphthalen-1-yl)prop-2-enamide [Bacillus cereus],5NC6_C Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (E)-N-hydroxy-3-(naphthalen-1-yl)prop-2-enamide [Bacillus cereus],5NC6_D Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (E)-N-hydroxy-3-(naphthalen-1-yl)prop-2-enamide [Bacillus cereus]
7FBW_A	5.41e-28	64	255	110	298	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
Q81EJ6	1.53e-34	60	266	54	271	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
O07596	8.26e-32	71	259	85	279	Putative polysaccharide deacetylase YheN OS=Bacillus subtilis (strain 168) OX=224308 GN=yheN PE=3 SV=1
Q81AF4	2.10e-21	71	255	22	207	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
O34798	4.59e-20	71	260	278	461	Peptidoglycan-N-acetylmuramic acid deacetylase PdaC OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaC PE=1 SV=1
Q8DP63	2.87e-19	67	255	264	446	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
0.629669	0.358089	0.004110	0.001938	0.001045	0.005137

TMHMM  Annotations     

start	end
10	32