serpentine, isoform C [Drosophila melanogaster]
Protein Classification
LDL receptor domain-containing protein( domain architecture ID 10482832)
Low Density Lipoprotein (LDL) receptor class A domain is a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| CE4_CDA_like_1 | cd10974 | Putative catalytic domain of chitin deacetylase-like proteins with additional chitin-binding ... |
200-475 | 0e+00 | |||||
Putative catalytic domain of chitin deacetylase-like proteins with additional chitin-binding peritrophin-A domain (ChBD) and/or a low-density lipoprotein receptor class A domain (LDLa); Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the N-deacetylation of chitin, a beta-1,4-linked N-acetylglucosamine polymer, to form chitosan, a polymer of beta-(1,4)-linked d-glucosamine residues. CDAs have been isolated and characterized from various bacterial and fungal species and belong to the larger carbohydrate esterase 4 (CE4) superfamily. This family includes many CDA-like proteins mainly from insects, which contain a putative CDA-like catalytic domain similar to the catalytic NodB homology domain of CE4 esterases. In addition to the CDA-like domain, family members contain two additional domains, a chitin-binding peritrophin-A domain (ChBD) and a low-density lipoprotein receptor class A domain (LDLa), or have the ChBD domain but do not have the LDLa domain. : Pssm-ID: 200596 Cd Length: 269 Bit Score: 514.96 E-value: 0e+00
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
125-159 | 2.79e-09 | |||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure : Pssm-ID: 238060 Cd Length: 35 Bit Score: 52.59 E-value: 2.79e-09
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| CBM_14 | pfam01607 | Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is ... |
48-105 | 1.37e-08 | |||||
Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains. : Pssm-ID: 426342 [Multi-domain] Cd Length: 53 Bit Score: 50.88 E-value: 1.37e-08
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| Name | Accession | Description | Interval | E-value | |||||
| CE4_CDA_like_1 | cd10974 | Putative catalytic domain of chitin deacetylase-like proteins with additional chitin-binding ... |
200-475 | 0e+00 | |||||
Putative catalytic domain of chitin deacetylase-like proteins with additional chitin-binding peritrophin-A domain (ChBD) and/or a low-density lipoprotein receptor class A domain (LDLa); Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the N-deacetylation of chitin, a beta-1,4-linked N-acetylglucosamine polymer, to form chitosan, a polymer of beta-(1,4)-linked d-glucosamine residues. CDAs have been isolated and characterized from various bacterial and fungal species and belong to the larger carbohydrate esterase 4 (CE4) superfamily. This family includes many CDA-like proteins mainly from insects, which contain a putative CDA-like catalytic domain similar to the catalytic NodB homology domain of CE4 esterases. In addition to the CDA-like domain, family members contain two additional domains, a chitin-binding peritrophin-A domain (ChBD) and a low-density lipoprotein receptor class A domain (LDLa), or have the ChBD domain but do not have the LDLa domain. Pssm-ID: 200596 Cd Length: 269 Bit Score: 514.96 E-value: 0e+00
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| CDA1 | COG0726 | Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ... |
192-313 | 2.60e-11 | |||||
Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis]; Pssm-ID: 440490 [Multi-domain] Cd Length: 195 Bit Score: 62.76 E-value: 2.60e-11
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| Polysacc_deac_1 | pfam01522 | Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of ... |
192-311 | 5.77e-10 | |||||
Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase. It also includes chitin deacetylase from yeast, and endoxylanases which hydrolyses glucosidic bonds in xylan. Pssm-ID: 426305 [Multi-domain] Cd Length: 124 Bit Score: 57.24 E-value: 5.77e-10
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
125-159 | 2.79e-09 | |||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 52.59 E-value: 2.79e-09
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| CBM_14 | pfam01607 | Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is ... |
48-105 | 1.37e-08 | |||||
Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains. Pssm-ID: 426342 [Multi-domain] Cd Length: 53 Bit Score: 50.88 E-value: 1.37e-08
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
125-156 | 5.32e-08 | |||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 48.78 E-value: 5.32e-08
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
125-159 | 2.49e-06 | |||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 44.16 E-value: 2.49e-06
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| ChtBD2 | smart00494 | Chitin-binding domain type 2; |
64-99 | 6.46e-05 | |||||
Chitin-binding domain type 2; Pssm-ID: 214696 [Multi-domain] Cd Length: 49 Bit Score: 40.50 E-value: 6.46e-05
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| Name | Accession | Description | Interval | E-value | |||||
| CE4_CDA_like_1 | cd10974 | Putative catalytic domain of chitin deacetylase-like proteins with additional chitin-binding ... |
200-475 | 0e+00 | |||||
Putative catalytic domain of chitin deacetylase-like proteins with additional chitin-binding peritrophin-A domain (ChBD) and/or a low-density lipoprotein receptor class A domain (LDLa); Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the N-deacetylation of chitin, a beta-1,4-linked N-acetylglucosamine polymer, to form chitosan, a polymer of beta-(1,4)-linked d-glucosamine residues. CDAs have been isolated and characterized from various bacterial and fungal species and belong to the larger carbohydrate esterase 4 (CE4) superfamily. This family includes many CDA-like proteins mainly from insects, which contain a putative CDA-like catalytic domain similar to the catalytic NodB homology domain of CE4 esterases. In addition to the CDA-like domain, family members contain two additional domains, a chitin-binding peritrophin-A domain (ChBD) and a low-density lipoprotein receptor class A domain (LDLa), or have the ChBD domain but do not have the LDLa domain. Pssm-ID: 200596 Cd Length: 269 Bit Score: 514.96 E-value: 0e+00
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| CE4_CDA_like | cd10919 | Putative catalytic domain of chitin deacetylase-like proteins from insects and similar ... |
200-475 | 3.34e-110 | |||||
Putative catalytic domain of chitin deacetylase-like proteins from insects and similar proteins; Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the N-deacetylation of chitin, a beta-1,4-linked N-acetylglucosamine polymer, to form chitosan, a polymer of beta-(1,4)-linked d-glucosamine residues. CDAs have been isolated and characterized from various bacterial and fungal species and belong to the larger carbohydrate esterase family 4 (CE4). This family includes many CDA-like proteins, mainly from insects, which contain a putative CDA-like catalytic domain similar to the catalytic NodB homology domain of CE4 esterases. Some family members have an additional chitin binding domain (ChBD), or an additional low-density lipoprotein receptor class A domain (LDLa), or both. Due to the lack of some catalytically relevant residues, several insect CDA-like proteins are devoid of enzymatic activity and may simply bind to chitin and thus influence the mechanical or permeability properties of chitin-containing structures such as the cuticle or the peritrophic membrane. This family also includes many uncharacterized hypothetical proteins from bacteria, exhibiting high sequence similarity to insect CDA-like proteins. Pssm-ID: 200545 [Multi-domain] Cd Length: 273 Bit Score: 329.32 E-value: 3.34e-110
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| CE4_CDA_like_2 | cd10975 | Putative catalytic domain of chitin deacetylase-like proteins; Chitin deacetylases (CDAs, EC 3. ... |
200-475 | 9.02e-108 | |||||
Putative catalytic domain of chitin deacetylase-like proteins; Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the N-deacetylation of chitin, a beta-1,4-linked N-acetylglucosamine polymer, to form chitosan, a polymer of beta-(1,4)-linked d-glucosamine residues. CDAs have been isolated and characterized from various bacterial and fungal species and belong to the larger carbohydrate esterase 4 (CE4) superfamily. This family includes many midgut-specific CDA-like proteins mainly from insects, such as Tribolium castaneum CDAs (TcCDA6-9). These proteins contain a putative CDA-like catalytic domain similar to the catalytic NodB homology domain of CE4 esterases. In addition to the CDA-like domain, some family members have an additional chitin-binding peritrophin-A domain (ChBD). Pssm-ID: 200597 Cd Length: 268 Bit Score: 322.73 E-value: 9.02e-108
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| CE4_CDA_like_3 | cd10976 | Putative catalytic domain of uncharacterized bacterial hypothetical proteins similar to insect ... |
255-477 | 3.06e-12 | |||||
Putative catalytic domain of uncharacterized bacterial hypothetical proteins similar to insect chitin deacetylase-like proteins; The family includes many uncharacterized bacterial hypothetical proteins that show high sequence similarity to insect chitin deacetylase-like proteins. Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the N-deacetylation of chitin, a beta-1,4-linked N-acetylglucosamine polymer, to form chitosan, a polymer of beta-(1,4)-linked d-glucosamine residues. Pssm-ID: 200598 [Multi-domain] Cd Length: 299 Bit Score: 67.38 E-value: 3.06e-12
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| CDA1 | COG0726 | Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ... |
192-313 | 2.60e-11 | |||||
Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis]; Pssm-ID: 440490 [Multi-domain] Cd Length: 195 Bit Score: 62.76 E-value: 2.60e-11
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| Polysacc_deac_1 | pfam01522 | Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of ... |
192-311 | 5.77e-10 | |||||
Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase. It also includes chitin deacetylase from yeast, and endoxylanases which hydrolyses glucosidic bonds in xylan. Pssm-ID: 426305 [Multi-domain] Cd Length: 124 Bit Score: 57.24 E-value: 5.77e-10
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
125-159 | 2.79e-09 | |||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 52.59 E-value: 2.79e-09
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| CE4_CtAXE_like | cd10954 | Catalytic NodB homology domain of Clostridium thermocellum acetylxylan esterase and its ... |
202-317 | 7.68e-09 | |||||
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. Pssm-ID: 200578 [Multi-domain] Cd Length: 180 Bit Score: 55.28 E-value: 7.68e-09
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| CBM_14 | pfam01607 | Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is ... |
48-105 | 1.37e-08 | |||||
Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains. Pssm-ID: 426342 [Multi-domain] Cd Length: 53 Bit Score: 50.88 E-value: 1.37e-08
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
125-156 | 5.32e-08 | |||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 48.78 E-value: 5.32e-08
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| CE4_PuuE_HpPgdA_like_2 | cd10941 | Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar ... |
234-432 | 6.19e-08 | |||||
Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA); This family contains many uncharacterized prokaryotic polysaccharide deacetylases (DCAs) that show high sequence similarity to the catalytic domain of bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA). PuuE allantoinase appears to be metal-independent and specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. Different from PuuE allantoinase, HpPgdA has the ability to bind a metal ion at the active site and is responsible for a peptidoglycan modification that counteracts the host immune response. Both PuuE allantoinase and HpPgdA function as homotetramers. The monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of DCA-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. In contrast to typical NodB-like DCAs, PuuE allantoinase and HpPgdA do not exhibit a solvent-accessible polysaccharide binding groove and might only bind a small molecule at the active site. Pssm-ID: 200566 [Multi-domain] Cd Length: 258 Bit Score: 53.83 E-value: 6.19e-08
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| CE4_SF | cd10585 | Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate ... |
202-335 | 1.30e-07 | |||||
Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate esterase 4 (CE4) superfamily mainly includes 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, respectively. Members in this superfamily contain a NodB homology domain that adopts a deformed (beta/alpha)8 barrel fold, which encompasses a mononuclear metalloenzyme employing 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. The NodB homology domain of CE4 superfamily is remotely related to the 7-stranded beta/alpha barrel catalytic domain of the superfamily consisting of family 38 glycoside hydrolases (GH38), family 57 heat stable retaining glycoside hydrolases (GH57), lactam utilization protein LamB/YcsF family proteins, and YdjC-family proteins. Pssm-ID: 213020 [Multi-domain] Cd Length: 142 Bit Score: 50.91 E-value: 1.30e-07
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| CE4_GLA_like_6s | cd10967 | Putative catalytic NodB homology domain of gellan lyase and similar proteins; This family is ... |
201-315 | 1.38e-07 | |||||
Putative catalytic NodB homology domain of gellan lyase and similar proteins; This family is represented by the extracellular polysaccharide-degrading enzyme, gellan lyase (gellanase, EC 4.2.2.-), from Bacillus sp. The enzyme acts on gellan exolytically and releases a tetrasaccharide of glucuronyl-glucosyl-rhamnosyl-glucose with unsaturated glucuronic acid at the nonreducing terminus. The family also includes many uncharacterized prokaryotic polysaccharide deacetylases, which show high sequence similarity to Bacillus sp. gellan lyase. Although their biological functions remain unknown, all members of the family contain a conserved domain with a 6-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily. Pssm-ID: 200589 [Multi-domain] Cd Length: 202 Bit Score: 52.00 E-value: 1.38e-07
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| CE4_NodB_like_6s_7s | cd10917 | Catalytic NodB homology domain of rhizobial NodB-like proteins; This family belongs to the ... |
203-314 | 2.67e-07 | |||||
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. Pssm-ID: 213022 [Multi-domain] Cd Length: 171 Bit Score: 50.70 E-value: 2.67e-07
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| CE4_SmPgdA_like | cd10944 | Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, ... |
206-326 | 5.68e-07 | |||||
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. Pssm-ID: 200569 [Multi-domain] Cd Length: 189 Bit Score: 49.85 E-value: 5.68e-07
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
125-159 | 2.49e-06 | |||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 44.16 E-value: 2.49e-06
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| CE4_HpPgdA_like | cd10938 | Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar ... |
233-332 | 1.88e-05 | |||||
Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar proteins; This family is represented by a peptidoglycan deacetylase (HP0310, HpPgdA) from the gram-negative pathogen Helicobacter pylori. HpPgdA has the ability to bind a metal ion at the active site and is responsible for a peptidoglycan modification that counteracts the host immune response. It functions as a homotetramer. The monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of polysaccharide deacetylase (DCA)-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. In contrast to typical NodB-like DCAs, HpPgdA does not exhibit a solvent-accessible polysaccharide binding groove, suggesting that the enzyme binds a small molecule at the active site. Pssm-ID: 200563 [Multi-domain] Cd Length: 258 Bit Score: 46.40 E-value: 1.88e-05
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| CE4_PuuE_HpPgdA_like | cd10916 | Catalytic domain of bacterial PuuE allantoinases, Helicobacter pylori peptidoglycan ... |
234-471 | 4.88e-05 | |||||
Catalytic domain of bacterial PuuE allantoinases, Helicobacter pylori peptidoglycan deacetylase (HpPgdA), and similar proteins; This family is a member of the very large and functionally diverse carbohydrate esterase 4 (CE4) superfamily. It contains bacterial PuuE (purine utilization E) allantoinases, a peptidoglycan deacetylase from Helicobacter pylori (HpPgdA), Escherichia coli ArnD, and many uncharacterized homologs from all three kingdoms of life. PuuE allantoinase appears to be metal-independent and specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. Different from PuuE allantoinase, HpPgdA has the ability to bind a metal ion at the active site and is responsible for a peptidoglycan modification that counteracts the host immune response. Both PuuE allantoinase and HpPgdA function as a homotetramer. The monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of polysaccharide deacetylase (DCA)-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. However, in contrast with the typical DCAs, PuuE allantoinase and HpPgdA might not exhibit a solvent-accessible polysaccharide binding groove and only recognize a small substrate molecule. ArnD catalyzes the deformylation of 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol. Pssm-ID: 213021 [Multi-domain] Cd Length: 247 Bit Score: 44.99 E-value: 4.88e-05
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| ChtBD2 | smart00494 | Chitin-binding domain type 2; |
64-99 | 6.46e-05 | |||||
Chitin-binding domain type 2; Pssm-ID: 214696 [Multi-domain] Cd Length: 49 Bit Score: 40.50 E-value: 6.46e-05
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| CE4_Sll1306_like | cd10978 | Putative catalytic domain of Synechocystis sp. Sll1306 protein and other bacterial homologs; ... |
251-349 | 1.01e-04 | |||||
Putative catalytic domain of Synechocystis sp. Sll1306 protein and other bacterial homologs; The family contains Synechocystis sp. Sll1306 protein and uncharacterized bacterial polysaccharide deacetylases. Although their biological function remains unknown, they show very high sequence homology to the catalytic domain of bacterial PuuE (purine utilization E) allantoinases. PuuE allantoinase specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. It functions as a homotetramer. Its monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of polysaccharide deacetylase-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. PuuE allantoinase appears to be metal-independent and acts on a small substrate molecule, which is distinct from the common feature of polysaccharide deacetylases that are normally metal ion dependent and recognize multimeric substrates. Pssm-ID: 200600 [Multi-domain] Cd Length: 271 Bit Score: 44.37 E-value: 1.01e-04
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| CE4_BH1302_like | cd10956 | Putative catalytic NodB homology domain of uncharacterized BH1302 protein from Bacillus ... |
203-268 | 2.32e-04 | |||||
Putative catalytic NodB homology domain of uncharacterized BH1302 protein from Bacillus halodurans and its bacterial homologs; This family is represented by a putative polysaccharide deacetylase BH1302 from Bacillus halodurans. Although its biological function is unknown, BH1302 shows 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. Both BH1302 and SpPgdA belong to the carbohydrate esterase 4 (CE4) superfamily. This family also includes many uncharacterized bacterial polysaccharide deacetylases. Pssm-ID: 200580 [Multi-domain] Cd Length: 194 Bit Score: 42.33 E-value: 2.32e-04
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| CE4_MrCDA_like | cd10952 | Catalytic NodB homology domain of Mucor rouxii chitin deacetylase and similar proteins; This ... |
205-267 | 3.32e-04 | |||||
Catalytic NodB homology domain of Mucor rouxii chitin deacetylase and similar proteins; This family is represented by the chitin deacetylase (MrCDA, EC 3.5.1.41) encoded from the fungus Mucor rouxii (also known as Amylomyces rouxii). MrCDA is an acidic glycoprotein with a very stringent specificity for beta1-4-linked N-acetylglucosamine homopolymers. It requires at least four residues (chitotetraose) for catalysis, and can achieve extensive deacetylation on chitin polymers. MrCDA shows high sequence similarity to Colletotrichum lindemuthianum chitin deacetylase (endo-chitin de-N-acetylase, ClCDA), which consists of a single catalytic domain similar to the deformed (beta/alpha)8 barrel fold adopted by the carbohydrate esterase 4 (CE4) superfamily, which encompasses a mononuclear metalloenzyme employing 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. The family also includes some uncharacterized eukaryotic and bacterial homologs of MrCDA. Pssm-ID: 200576 [Multi-domain] Cd Length: 178 Bit Score: 41.58 E-value: 3.32e-04
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| CE4_SpPgdA_BsYjeA_like | cd10947 | Catalytic NodB homology domain of Streptococcus pneumoniae peptidoglycan deacetylase PgdA, ... |
203-311 | 5.42e-04 | |||||
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. Pssm-ID: 200571 [Multi-domain] Cd Length: 177 Bit Score: 41.22 E-value: 5.42e-04
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| CE4_NodB_like_5s_6s | cd10918 | Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a ... |
205-304 | 1.14e-03 | |||||
Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; 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 bacterial poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, hemin storage system HmsF protein in gram-negative species, intercellular adhesion proteins IcaB, and many uncharacterized prokaryotic polysaccharide deacetylases. It also includes a putative polysaccharide deacetylase YxkH encoded by the Bacillus subtilis yxkH gene, which is one of six polysaccharide deacetylase gene homologs present in the Bacillus subtilis genome. Sequence comparison shows all family members contain a conserved domain similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, which consists of a deformed (beta/alpha)8 barrel fold with 6 or 7 strands. However, in this family, most proteins have 5 strands and some have 6 strands. Moreover, long insertions are found in many family members, whose function remains unknown. Pssm-ID: 213023 [Multi-domain] Cd Length: 157 Bit Score: 39.89 E-value: 1.14e-03
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| CE4_Mll8295_like | cd10946 | Putative catalytic NodB homology domain of uncharacterized Mll8295 protein encoded from ... |
203-277 | 5.28e-03 | |||||
Putative catalytic NodB homology domain of uncharacterized Mll8295 protein encoded from Rhizobium loti and its bacterial homologs; This family is represented by a putative polysaccharide deacetylase Mll8295 encoded from Rhizobium loti. Although its biological function still remains unknown, Mll8295 shows high sequence homology to the catalytic 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. Both Mll8295 and SpPgdA belong to the carbohydrate esterase 4 (CE4) superfamily. This family also includes many uncharacterized bacterial polysaccharide deacetylases. Pssm-ID: 200570 [Multi-domain] Cd Length: 217 Bit Score: 38.54 E-value: 5.28e-03
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