putative 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD [Escherichia coli str. K-12 substr. MG1655]
Protein Classification
4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase( domain architecture ID 11487769)
4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD catalyzes the formation of 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol from 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| PRK15394 | PRK15394 | 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional |
1-291 | 0e+00 | |||||
4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional : Pssm-ID: 185292 Cd Length: 296 Bit Score: 597.68 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | |||||
| PRK15394 | PRK15394 | 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional |
1-291 | 0e+00 | |||||
4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional Pssm-ID: 185292 Cd Length: 296 Bit Score: 597.68 E-value: 0e+00
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| CE4_ArnD | cd10939 | Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol ... |
3-288 | 2.16e-166 | |||||
Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD and other bacterial homologs; This family is represented by Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD (EC 3.5.1.n3). ArnD plays an important role in the biosynthesis of undecaprenyl phosphate alpha-4-amino-4-deoxy-L-arabinose (alpha-L-Ara4N). It catalyzes the deformylation of 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol. The ArnD-dependent deformylation likely occurs on the inner leaflet of the inner membrane. This family also includes many uncharacterized bacterial polysaccharide deacetylases. All family members show high sequence homology to the catalytic domain of bacterial PuuE (purine utilization E) allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA), and are classified within the larger carbohydrate esterase 4 (CE4) superfamily. Pssm-ID: 200564 [Multi-domain] Cd Length: 290 Bit Score: 463.30 E-value: 2.16e-166
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| CDA1 | COG0726 | Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ... |
4-264 | 2.42e-17 | |||||
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: 78.16 E-value: 2.42e-17
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| Polysacc_deac_1 | pfam01522 | Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of ... |
15-145 | 1.23e-06 | |||||
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: 46.84 E-value: 1.23e-06
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| Name | Accession | Description | Interval | E-value | |||||
| PRK15394 | PRK15394 | 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional |
1-291 | 0e+00 | |||||
4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional Pssm-ID: 185292 Cd Length: 296 Bit Score: 597.68 E-value: 0e+00
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| CE4_ArnD | cd10939 | Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol ... |
3-288 | 2.16e-166 | |||||
Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD and other bacterial homologs; This family is represented by Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD (EC 3.5.1.n3). ArnD plays an important role in the biosynthesis of undecaprenyl phosphate alpha-4-amino-4-deoxy-L-arabinose (alpha-L-Ara4N). It catalyzes the deformylation of 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol. The ArnD-dependent deformylation likely occurs on the inner leaflet of the inner membrane. This family also includes many uncharacterized bacterial polysaccharide deacetylases. All family members show high sequence homology to the catalytic domain of bacterial PuuE (purine utilization E) allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA), and are classified within the larger carbohydrate esterase 4 (CE4) superfamily. Pssm-ID: 200564 [Multi-domain] Cd Length: 290 Bit Score: 463.30 E-value: 2.16e-166
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| CE4_SF | cd10585 | Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate ... |
3-173 | 1.36e-23 | |||||
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: 93.67 E-value: 1.36e-23
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| CDA1 | COG0726 | Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ... |
4-264 | 2.42e-17 | |||||
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: 78.16 E-value: 2.42e-17
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| CE4_PuuE_HpPgdA_like_2 | cd10941 | Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar ... |
14-233 | 2.36e-13 | |||||
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: 68.47 E-value: 2.36e-13
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| Polysacc_deac_1 | pfam01522 | Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of ... |
15-145 | 1.23e-06 | |||||
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: 46.84 E-value: 1.23e-06
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| CE4_PuuE_HpPgdA_like | cd10916 | Catalytic domain of bacterial PuuE allantoinases, Helicobacter pylori peptidoglycan ... |
15-154 | 2.52e-06 | |||||
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: 47.69 E-value: 2.52e-06
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| CE4_BsYlxY_like | cd10950 | Putative catalytic NodB homology domain of uncharacterized protein YlxY from Bacillus subtilis ... |
3-168 | 2.66e-06 | |||||
Putative catalytic NodB homology domain of uncharacterized protein YlxY from Bacillus subtilis and its bacterial homologs; The Bacillus subtilis genome contains six polysaccharide deacetylase gene homologs: pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH and ylxY. This family is represented by Bacillus subtilis putative polysaccharide deacetylase BsYlxY, encoded by the ylxY gene, which is a member of the carbohydrate esterase 4 (CE4) superfamily. Although its biological function still remains unknown, BsYlxY shows high sequence homology to the catalytic domain of Bacillus subtilis pdaB gene encoding a putative polysaccharide deacetylase (BsPdaB), which is essential for the maintenance of spores after the late stage of sporulation and is highly conserved in spore-forming bacteria. However, disruption of the ylxY gene in B. subtilis did not cause any sporulation defect. Moreover, the Asp residue in the classical His-His-Asp zinc-binding motif of CE4 esterases is mutated to a Val residue in this family. Other catalytically relevant residues of CE4 esterases are also not conserved, which suggest that members of this family may be inactive. Pssm-ID: 200574 [Multi-domain] Cd Length: 188 Bit Score: 46.89 E-value: 2.66e-06
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| CE4_NodB_like_6s_7s | cd10917 | Catalytic NodB homology domain of rhizobial NodB-like proteins; This family belongs to the ... |
12-169 | 5.27e-06 | |||||
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: 45.69 E-value: 5.27e-06
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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 ... |
24-145 | 5.59e-06 | |||||
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: 45.67 E-value: 5.59e-06
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| CE4_HpPgdA_like | cd10938 | Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar ... |
15-195 | 1.12e-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: 45.63 E-value: 1.12e-05
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| CE4_GLA_like_6s | cd10967 | Putative catalytic NodB homology domain of gellan lyase and similar proteins; This family is ... |
90-145 | 8.01e-04 | |||||
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: 39.67 E-value: 8.01e-04
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| CE4_u5 | cd10929 | Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase ... |
11-41 | 5.98e-03 | |||||
Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily; This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. Pssm-ID: 200555 [Multi-domain] Cd Length: 263 Bit Score: 37.63 E-value: 5.98e-03
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