Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; Allantoinase (EC 3.5.2.5) can hydrolyze allantoin((2,5-dioxoimidazolidin-4-yl)urea), one of the most important nitrogen carrier for some plants, soil animals, and microorganisms, to allantoate. DAL1 gene from Saccharomyces cerevisiae encodes an allantoinase. However, some organisms possess allantoinase activity but lack DAL1 allantoinase. In those organisms, a defective allantoinase gene, named puuE (purine utilization E), encodes an allantoinase that specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. PuuE allantoinase is related to polysaccharide deacetylase (DCA), one member of the carbohydrate esterase 4 (CE4) superfamily, that removes N-linked or O-linked acetyl groups of cell wall polysaccharides, and lacks sequence similarity with the known DAL1 allantoinase that belongs to the amidohydrolase superfamily. PuuE allantoinase 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 DCAs. It appears to be metal-independent and acts on a small substrate molecule, which is distinct from the common features of DCAs that are normally metal ion dependent and recognize multimeric substrates. This family also includes a chitin deacetylase 1 (SpCDA1) encoded by the Schizosaccharomyces pombe cda1 gene. Although the general function of chitin deacetylase (CDA) is the synthesis of chitosan from chitin, a polymer of N-acetyl glucosamine, to build up the proper ascospore wall, the actual function of SpCDA1 might involve allantoin hydrolysis. It is likely orthologous to PuuE allantoinase, whereas it is more distantly related to the CDAs found in other fungi, such as Saccharomyces cerevisiae and Mucor rouxii. Those CDAs are similar with rizobial NodB protein and are not included in this family.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  21 WPGDARIALSFVLNYEEGGERCVLHGDKESEAFLSEMVAAqPLQGVRHMSMESLYEYGSRAGVWRLLKLFKRRNVPLTVF 100
Cdd:cd10977   1 WPGGARVAVSFVLNYEEGGERSILHGDGASESFLSEIVGA-PLPGVRDLSMESLYEYGSRAGVWRILRLFDRRDVPLTVF 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714 101 AVAMAAQRNPEVIRAMVADGHEICSHGYRWIDYQYMDEAQEREHMLEAIRILTELTGQRPVGWYTGRTGPNTRRLVMEEG 180
Cdd:cd10977  80 AVAMALERNPAVARAMVAAGHEIASHGWRWIDYQGMDEAEEREHIRRAIAIIERLTGERPLGWYTGRASPNTRRLVVEEG 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714 181 GFLYDSDTYDDDLPYWDPAStaEKPHLVIPYTLDTNDMRFTQVQGFNNGEQFFQYLKDAFDVLYEEGATAPKMLSIGLHC 260
Cdd:cd10977 160 GFLYDSDSYDDDLPYWVDVE--GKPHLVVPYTLDTNDMRFATAQGFNTADDFFTYLKDAFDVLYEEGAEAPKMMSIGLHC 237

                       250       260       270
                ....*....|....*....|....*....|....*.
gi 15596714 261 RLIGRPARMAALERFIQYAQSHDKVWFARREDIARH 296
Cdd:cd10977 238 RLIGRPGRFAGLERFLEHVKSHDGVWVARREDIARH 273

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714    75 YEYGSRAGVWRLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYRWIDYQYMDEAQEREHMLEAIRILTE 154
Cdd:pfam01522  13 FDDGPSENTPAILDVLKKYGVKATFFVIGGNVERYPDLVKRMVEAGHEIGNHTWSHPNLTGLSPEEIRKEIERAQDALEK 92

                          90       100       110
                  ....*....|....*....|....*....|.
gi 15596714   155 LTGQRPVGW-YTGRTGPNTRRLVMEEGGFLY 184
Cdd:pfam01522  93 ATGKRPRLFrPPYGSYNDTVLEVAKKLGYTA 123

Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; Allantoinase (EC 3.5.2.5) can hydrolyze allantoin((2,5-dioxoimidazolidin-4-yl)urea), one of the most important nitrogen carrier for some plants, soil animals, and microorganisms, to allantoate. DAL1 gene from Saccharomyces cerevisiae encodes an allantoinase. However, some organisms possess allantoinase activity but lack DAL1 allantoinase. In those organisms, a defective allantoinase gene, named puuE (purine utilization E), encodes an allantoinase that specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. PuuE allantoinase is related to polysaccharide deacetylase (DCA), one member of the carbohydrate esterase 4 (CE4) superfamily, that removes N-linked or O-linked acetyl groups of cell wall polysaccharides, and lacks sequence similarity with the known DAL1 allantoinase that belongs to the amidohydrolase superfamily. PuuE allantoinase 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 DCAs. It appears to be metal-independent and acts on a small substrate molecule, which is distinct from the common features of DCAs that are normally metal ion dependent and recognize multimeric substrates. This family also includes a chitin deacetylase 1 (SpCDA1) encoded by the Schizosaccharomyces pombe cda1 gene. Although the general function of chitin deacetylase (CDA) is the synthesis of chitosan from chitin, a polymer of N-acetyl glucosamine, to build up the proper ascospore wall, the actual function of SpCDA1 might involve allantoin hydrolysis. It is likely orthologous to PuuE allantoinase, whereas it is more distantly related to the CDAs found in other fungi, such as Saccharomyces cerevisiae and Mucor rouxii. Those CDAs are similar with rizobial NodB protein and are not included in this family.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  21 WPGDARIALSFVLNYEEGGERCVLHGDKESEAFLSEMVAAqPLQGVRHMSMESLYEYGSRAGVWRLLKLFKRRNVPLTVF 100
Cdd:cd10977   1 WPGGARVAVSFVLNYEEGGERSILHGDGASESFLSEIVGA-PLPGVRDLSMESLYEYGSRAGVWRILRLFDRRDVPLTVF 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714 101 AVAMAAQRNPEVIRAMVADGHEICSHGYRWIDYQYMDEAQEREHMLEAIRILTELTGQRPVGWYTGRTGPNTRRLVMEEG 180
Cdd:cd10977  80 AVAMALERNPAVARAMVAAGHEIASHGWRWIDYQGMDEAEEREHIRRAIAIIERLTGERPLGWYTGRASPNTRRLVVEEG 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714 181 GFLYDSDTYDDDLPYWDPAStaEKPHLVIPYTLDTNDMRFTQVQGFNNGEQFFQYLKDAFDVLYEEGATAPKMLSIGLHC 260
Cdd:cd10977 160 GFLYDSDSYDDDLPYWVDVE--GKPHLVVPYTLDTNDMRFATAQGFNTADDFFTYLKDAFDVLYEEGAEAPKMMSIGLHC 237

                       250       260       270
                ....*....|....*....|....*....|....*.
gi 15596714 261 RLIGRPARMAALERFIQYAQSHDKVWFARREDIARH 296
Cdd:cd10977 238 RLIGRPGRFAGLERFLEHVKSHDGVWVARREDIARH 273

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  28 ALSFVLNYEEGGERCVLHGDKESeaflsemvaaqplqgvrhMSMESLYEYGSRAGVWRLLKLFKRRNVPLTVFAVAMAAQ 107
Cdd:cd10916   1 AVSVTVDVEGWAGGAASHGAPMA------------------PAAYSWGRYGLRVGIPRLLDLLDRHGVRATFFVPGRVAE 62

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714 108 RNPEVIRAMVADGHEICSHGYRWIDYQYMDEAQEREHMLEAIRILTELTGQRPVGWYTGRTG--PNTRRLVMEEgGFLYD 185
Cdd:cd10916  63 RFPDAVRAIVAAGHEIAAHGYAHEDVLALSREQEREVLLRSLELLEELTGQRPTGWRSPGLTfsPDTLELLAEL-GYLYD 141

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714 186 SDTYDDDLPYWDPASTAEKPHLVIPYTLDTNDMRFTQVQGFnNGEQFFQYLKDAFDVLYEEGatapKMLSIGLHCRLIGR 265
Cdd:cd10916 142 GDTYDDDLPYYWRDATGGGPILELPYTTVLNDLRFFMGGGG-LPRAFYENWKEQFDVLYARG----RYLSLTLHPRVIGR 216

                       250       260       270
                ....*....|....*....|....*....|.
gi 15596714 266 PARMAALERFIQYAQSHDKVWFARREDIARH 296
Cdd:cd10916 217 PARAAALDRFLRYVKSHPDVWFATHDEIARH 247

Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases; The family includes a group of uncharacterized prokaryotic polysaccharide deacetylases (DCAs) that show high sequence similarity 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 DCA-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 DCAs which are normally metal ion dependent and recognize multimeric substrates.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  15 NPPHPHWPGDARIALSFVLNYEeggercVLHGDKESEAFLSEMVAAQPlqGVRHMSmesLYEYGSRAGVWRLLKLFKRRN 94
Cdd:cd10979   8 DRPPLRWPGGARVAVWVAVNVE------HFPLDPPMPPILPAPATPYP--DVLNYS---WRDYGNRVGIWRLLDALDELG 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  95 VPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYRWIDYQY-MDEAQEREHMLEAIRILTELTGQRPVGWYT-GRT-GPN 171
Cdd:cd10979  77 IPPTVALNAAVADRYPELIEAIRERGWEFIAHGISNSTLHAgLDEAQEREVIAESLDRIEKATGQRPRGWLSpGLSeTEN 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714 172 TRRLvMEEGGFLYDSDTYDDDLPYWdpASTAEKPHLVIPYTLDTNDMRFTQVQGfNNGEQFFQYLKDAFDVLYEEGATAP 251
Cdd:cd10979 157 TPDL-LAEAGIEYLCDWVNDDQPYW--LRTPAGPLLSLPYTLELNDIPIYLVRG-HSADEFADRIIDQFDQLYAEGAESG 232

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*
gi 15596714 252 KMLSIGLHCRLIGRPARMAALERFIQYAQSHDKVWFARREDIARH 296
Cdd:cd10979 233 RVMAIALHPYIVGQPHRIRALEEALEYIAAHPDVWFATGGEIADW 277

Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  77 YGSRAGVWRLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYRWIDYQYMDEAQEREHMLEAIRILTELT 156
Cdd:COG0726  28 DGPREGTPRLLDLLKKYGVKATFFVVGSAVERHPELVREIAAAGHEIGNHTYTHPDLTKLSEEEERAEIARAKEALEELT 107

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15596714 157 GQRPVGWYT--GRTGPNTRRLVMEEgGFLY--DSDTYDDDLPYWDPASTAE------KPHLVIPYTLD 214
Cdd:COG0726 108 GKRPRGFRPpyGRYSPETLDLLAEL-GYRYilWDSVDSDDWPYPSADAIVDrvlkylKPGSIRPGTVE 174

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  62 PLQGVRHMSMESLYEYGSRAGVWRLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYRWIDYQYMDEAQE 141
Cdd:cd10941  13 HPYAFEGEIDWEDQERRLEEGLDRLLDLLDKHGVKATFFVLGEVAERYPDLIRRIAEAGHEIASHGYAHERVDRLTPEEF 92

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714 142 REHMLEAIRILTELTGQRPVGWYTGRTGPNTRRL-VMEEGGFLYDSDTYDDDLP-YWDPASTAEKPHLVI 209
Cdd:cd10941  93 REDLRRSKKILEDITGQKVVGFRAPNFSITPWALdILAEAGYLYDSSVFPTKRPgYGGPLAPKSEPLPPI 162

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  85 RLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYRWIDYQYMDEAQEREHMLEAIRILTELTGQRPVgWY 164
Cdd:cd10917  18 KILDILAEYGVKATFFVVGENVEKHPDLVRRIVAEGHEIGNHTYSHPDLTKLSPEEIRAEIERTQDAIEEATGVRPR-LF 96

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 15596714 165 ---TGRTGPNTRRLVMEEG--GFLYDSDTYDddlpyWDPASTAE 203
Cdd:cd10917  97 rppYGAYNPEVLAAAAELGltVVLWSVDSLD-----WKDPSPDQ 135

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  85 RLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYRWIDYQYMDEAQEREHMLEAIRILTELTGQRPV--- 161
Cdd:cd10959  18 ALLDLLARHGAKATFFVVGERAERHPDLIRRIVDEGHEIGNHGYRHRHPWLRSPWKAIRDLRRAARIIEQLTGRPPRyyr 97

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 15596714 162 ---GWYTGRTGPNTRRLVMEegGFLYDSDTYDddlpyWDPASTAEK 204
Cdd:cd10959  98 ppwGHLNLATLLAARRLGLK--IVLWSVDGGD-----WRPNATAAE 136

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  85 RLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYRWIDYQYMDEAQEREHMLEAIRILTELTGQRPVgWY 164
Cdd:cd10950  23 AMLTILEKHDVKATFFLEGRWAKKNPDLVRKIAKDGHEIGNHGYSHPDPSQLSYEQNREEIRKTNEIIEEITGEKPK-LF 101

                        90       100       110
                ....*....|....*....|....*....|.
gi 15596714 165 T---GRTGPNTRRLVMEEG--GFLYDSDTYD 190
Cdd:cd10950 102 AppyGEFNDAVVKAAAELGmrTILWTVDTID 132

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  85 RLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYRWIDYQYMDEAQEREHMLEAIRILTEL----TGQRP 160
Cdd:cd10942  38 RILDLLDELGIRCTYFVEGWSALHYPDELEAILAHGHEIGLHGWQHEPWAGLSPLEEDDLINRSLSIAERLglapVGFRP 117

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714 161 VGwytGRTGPNTRRLVMEEgGFLYDSdtydddlPYWDPASTAEKPH--LVIPYTLDTND-----MRFTQVQGFNNGE--- 230
Cdd:cd10942 118 PG---GALGAHTLALLAKH-GIRYVS-------LAGTGRSLATMPDglAVLPFAWAAVDgfyylDSFDGLRGPPQEEvdt 186

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15596714 231 --QFFQYLKDAFDVLYEEGAtapkMLSIGLHCRLIGRPARMAALERFIQYAQSHDKVWFARREDIA 294
Cdd:cd10942 187 paALAQALRSALDAVVARGG----FLTIVFHPFLSGSPERLAVFEQVLRRIANDSRIWCAPAREVA 248

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15596714  85 RLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYRWIDYQYMDEAQ---EREHMLEAIRiltELTGQRP 160
Cdd:cd10954  18 RLLDVLEKYNVRATFFLVGQNVNGNKEIVKRMVEMGCEIGNHSYTHPDLTKLSPSEikkEIEKTNEAIK---KITGKRP 93

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  85 RLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYrwiDYQYMDEAQEREHMLEAI---RILTELTGQRPV 161
Cdd:cd10962  18 QILDILKEYQIPATFFVIGENAVNNPELVKRIIDEGHEIGNHTF---THPDLDLLSEKRTRLELNatqRLIEAATGHSTL 94

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  85 RLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEIC----SHGYRWI---DYQYMDEaqerehMLEAIRILTELTG 157
Cdd:cd10944  17 KILDILKKYNVKATFFVIGSNVEKYPELVKRIVKEGHAIGlhsyTHDYKKLyssPEAFIKD------LNKTQDLIKKITG 90

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15596714 158 QRPVGW---YTGRTGPNTRRLV--MEEGGFLY---DSDTYDDDLPYWDPAS--------TAEKPHLVI 209
Cdd:cd10944  91 VKTKLIrfpGGSSNTGLMKALRkaLTKRGYKYwdwNVDSGDAKGKPKSAEQivqnvikqVKNKNVIVI 158

Catalytic NodB homology domain of Bacillus subtilis polysaccharide deacetylase PdaA, 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 pdaA gene encoding polysaccharide deacetylase BsPdaA, which is a member of the carbohydrate esterase 4 (CE4) superfamily. BsPdaA deacetylates peptidoglycan N-acetylmuramic acid (MurNAc) residues to facilitate the formation of muramic delta-lactam, which is required for recognition of germination lytic enzymes. BsPdaA deficiency leads to the absence of muramic delta-lactam residues in the spore cortex. Like other CE4 esterases, BsPdaA consists of a single catalytic NodB homology domain that appears to adopt a deformed (beta/alpha)8 barrel fold with a putative substrate binding groove harboring the majority of the conserved residues. It utilizes a general acid/base catalytic mechanism involving a tetrahedral transition intermediate, where a water molecule functions as the nucleophile tightly associated to the zinc cofactor.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  75 YEYGSRAgvwRLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYRWIDYQYMDEAQEREHMLEAIRILTE 154
Cdd:cd10948  50 YENGYTP---KILDVLKKNDVKATFFVTGHYVKSNPDLIKRMVDEGHIIGNHTVHHPDMTTLSDEKFKKEITGVEEEYKE 126

                ....
gi 15596714 155 LTGQ 158
Cdd:cd10948 127 VTGK 130

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  85 RLLKLFKRRNVP----LTVFAVAMAAQRNPEVIRAMVADGHEICSHGYRWIDY-QYMDEAQEREhMLEAIRILTELTGQR 159
Cdd:cd10967  16 RAAPLLAKYGLKgtffVNSGLLGRRGYLDLEELRELAAAGHEIGSHTVTHPDLtSLPPAELRRE-IAESRAALEEIGGFP 94

                ...
gi 15596714 160 PVG 162
Cdd:cd10967  95 VTS 97

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714  65 GVRH-MSMESLYEY--GSRAGVWRLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVAD-GHEICSHGYRWIDYQY--MDE 138
Cdd:cd10929  14 GVRDkRSVPEYEENllGAREAIPRLLELFDEYNIPATWATVGFLFHFAPSLIDLIASTpGQEIGSHTFSHYYCLEegQTR 93

                        90
                ....*....|....
gi 15596714 139 AQEREHMLEAIRIL 152
Cdd:cd10929  94 EVFEADLEAAKKAA 107

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15596714  79 SRAGVWRLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYrwiDYQYM 136
Cdd:cd10956  16 TPAHTDAILSILDEYDIKATFFLIGREIEENPSEARAIVAAGHEIGNHSY---SHRRM 70

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 15596714  86 LLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYR 129
Cdd:cd10958  18 ILDLLEEHNVRATFFVIGSHAPRREEVLSRIVEEGHELGNHGMH 61

Uncharacterized protein conserved in bacteria (DUF2334); This domain, found in various hypothetical bacterial proteins, has no known function.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714    85 RLLKLFKRRNVPLTVF----------AVAMAAqrNPE---VIRAMVADGHEICSHGYRWI--------------DYQYMD 137
Cdd:pfam10096  20 AIADYLDAYGIPFSVAvipnykdpktKYNLSD--NPEfvnYLKYLQARGGEIALHGYTHQygtpngrysefsgvEFEFLS 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596714   138 EAQEREHMLEAIRILTELtGQRPVGW----YTGrtGPNTRRLVMEEGGFLYDSDTYDddlPYWDPASTaekphLVIPYTL 213
Cdd:pfam10096  98 EAEAKERIEKGIEILKKL-GIPPTGFeaphYAA--SPNTYKALKEYFTIIYDGFAYY---PYDQRYGF-----TYIPENL 166

                  .
gi 15596714   214 D 214
Cdd:pfam10096 167 G 167