dbCAN-seq: a database of CAZyme sequence and annotation

Basic Information help

Species

Parastagonospora nodorum

Lineage

Ascomycota; Dothideomycetes; ; Phaeosphaeriaceae; Parastagonospora; Parastagonospora nodorum

CAZyme ID

QRD01896.1

CAZy Family

GH3

CAZyme Description

NodB homology domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A7U2I3F2]

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
242		27319.57	9.6931

Genome Property

Genome Version/Assembly ID	Genes	Strain NCBI Taxon ID	Non Protein Coding Genes	Protein Coding Genes
FungiDB-61_PnodorumSN15	17580	321614	132	17448

Gene Location

Enzyme Prediction help

No EC number prediction in QRD01896.1.

CAZyme Signature Domains help

Family	Start	End	Evalue	family coverage
CE4	41	172	7.6e-20	0.9538461538461539

CDD Domains download full data without filtering help

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
200581	CE4_NodB_like_2	8.31e-87	45	232	1	190	Catalytic NodB homology domain of uncharacterized chitin deacetylases and hypothetical proteins. This family includes some uncharacterized chitin deacetylases and hypothetical proteins, mainly from eukaryotes. Although their biological function is unknown, members in this family show high sequence homology to the catalytic NodB homology domain of Colletotrichum lindemuthianum chitin deacetylase (endo-chitin de-N-acetylase, ClCDA, EC 3.5.1.41), which catalyzes the hydrolysis of N-acetamido groups of N-acetyl-D-glucosamine residues in chitin, converting it to chitosan in fungal cell walls. Like ClCDA, this family is a member the carbohydrate esterase 4 (CE4) superfamily.
213022	CE4_NodB_like_6s_7s	2.15e-41	45	220	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.
200578	CE4_CtAXE_like	2.35e-38	45	232	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.
200582	CE4_NodB_like_3	4.19e-35	45	229	1	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.
200584	CE4_GT2-like	1.85e-29	45	234	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 help

Hit ID	E-Value	Query Start	Query End	Hit Start
1.20e-175	1	242	1	242
2.09e-113	8	237	32	263
6.93e-113	7	239	7	249
8.51e-101	1	242	1	243
8.51e-101	1	242	1	243

PDB Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
2.97e-27	36	234	108	301	Chain A, Predicted xylanase/chitin deacetylase [Caldanaerobacter subterraneus subsp. tengcongensis MB4]
4.70e-19	44	234	3	187	Crystal structure of the Xyl-CE4 domain of a multidomain xylanase from the hindgut metagenome of Trinervitermes trinervoides [uncultured bacterium]
5.59e-19	47	233	42	227	Chain A, Aspergillus niger contig An12c0130, genomic contig [Aspergillus niger CBS 513.88]
3.85e-18	44	234	235	417	Structure of Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) [Streptococcus pneumoniae R6]
1.80e-17	44	234	235	417	Structure of Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) D 275 N Mutant. [Streptococcus pneumoniae R6]

Swiss-Prot Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
1.14e-27	36	233	13	209	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
1.52e-19	44	234	401	585	Bifunctional xylanase/deacetylase OS=Pseudobutyrivibrio xylanivorans OX=185007 GN=xyn11A PE=1 SV=2
2.20e-17	44	234	267	449	Peptidoglycan-N-acetylglucosamine deacetylase OS=Streptococcus pneumoniae (strain ATCC BAA-255 / R6) OX=171101 GN=pgdA PE=1 SV=1
3.61e-16	47	229	20	211	Chitooligosaccharide deacetylase OS=Sinorhizobium fredii (strain NBRC 101917 / NGR234) OX=394 GN=nodB PE=3 SV=2
1.92e-15	43	226	19	210	Chitooligosaccharide deacetylase OS=Rhizobium meliloti (strain 1021) OX=266834 GN=nodB PE=3 SV=3

SignalP and Lipop Annotations help

This protein is predicted as OTHER

Other	SP_Sec_SPI	CS Position
0.995171	0.004861

TMHMM Annotations download full data without filtering help

Start	End
2	19

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