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 302150204   1 MILLSFDTEEFDVPREHGVDFSLEEGMKVSIEGTNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVD 80
Cdd:cd10941    1 MNILTFDVEDWYHPYAFEGEIDWEDQERRLEEGLDRLLDLLDKHGVKATFFVLGEVAERYPDLIRRIAEAGHEIASHGYA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204  81 HWQPKP-------EDVFRSKEIIERVTGVKVAGYRQPRM--FPVSDEDIEKAGYLYNSSLNPAFIPGRYMHL----TTPR 147
Cdd:cd10941   81 HERVDRltpeefrEDLRRSKKILEDITGQKVVGFRAPNFsiTPWALDILAEAGYLYDSSVFPTKRPGYGGPLapksEPLP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204 148 TWFMQGKVMQIPASVSPH--LRIPLFWLS-MHNFPEWFYLRLVRQVLRHDGYFVTYFHPWEFYDLKSHPEFKMPFIIKNH 224
Cdd:cd10941  161 PIRAKGGILEFPVSVTKLpgLRLPLAGGGyFRLLPYRLIKALIKRSLRRGGPLVLYFHPWEFDPEQPVPGLPLLRRFRTY 240

                        250
                 ....*....|....*...
gi 302150204 225 SG-HELEQRLDRFIKAMK 241
Cdd:cd10941  241 VGlGKAEEKLERLLEDFK 258

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 302150204   1 MILLSFDTEEFDVPREHGVDFSLEEGMKVSIEGTNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVD 80
Cdd:cd10941    1 MNILTFDVEDWYHPYAFEGEIDWEDQERRLEEGLDRLLDLLDKHGVKATFFVLGEVAERYPDLIRRIAEAGHEIASHGYA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204  81 HWQPKP-------EDVFRSKEIIERVTGVKVAGYRQPRM--FPVSDEDIEKAGYLYNSSLNPAFIPGRYMHL----TTPR 147
Cdd:cd10941   81 HERVDRltpeefrEDLRRSKKILEDITGQKVVGFRAPNFsiTPWALDILAEAGYLYDSSVFPTKRPGYGGPLapksEPLP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204 148 TWFMQGKVMQIPASVSPH--LRIPLFWLS-MHNFPEWFYLRLVRQVLRHDGYFVTYFHPWEFYDLKSHPEFKMPFIIKNH 224
Cdd:cd10941  161 PIRAKGGILEFPVSVTKLpgLRLPLAGGGyFRLLPYRLIKALIKRSLRRGGPLVLYFHPWEFDPEQPVPGLPLLRRFRTY 240

                        250
                 ....*....|....*...
gi 302150204 225 SG-HELEQRLDRFIKAMK 241
Cdd:cd10941  241 VGlGKAEEKLERLLEDFK 258

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 302150204   1 MILLSFDteefDVPREhgvdfsleegmkvsieGTNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVD 80
Cdd:COG0726   21 AVALTFD----DGPRE----------------GTPRLLDLLKKYGVKATFFVVGSAVERHPELVREIAAAGHEIGNHTYT 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 302150204  81 HWQPKP-------EDVFRSKEIIERVTGVKVAGYRQP--RMFPVSDEDIEKAGYLY 127
Cdd:COG0726   81 HPDLTKlseeeerAEIARAKEALEELTGKRPRGFRPPygRYSPETLDLLAELGYRY 136

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 302150204   1 MILLSFDTEEFDVPREHGVDFSLEEGMKVSIEGTNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVD 80
Cdd:cd10941    1 MNILTFDVEDWYHPYAFEGEIDWEDQERRLEEGLDRLLDLLDKHGVKATFFVLGEVAERYPDLIRRIAEAGHEIASHGYA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204  81 HWQPKP-------EDVFRSKEIIERVTGVKVAGYRQPRM--FPVSDEDIEKAGYLYNSSLNPAFIPGRYMHL----TTPR 147
Cdd:cd10941   81 HERVDRltpeefrEDLRRSKKILEDITGQKVVGFRAPNFsiTPWALDILAEAGYLYDSSVFPTKRPGYGGPLapksEPLP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204 148 TWFMQGKVMQIPASVSPH--LRIPLFWLS-MHNFPEWFYLRLVRQVLRHDGYFVTYFHPWEFYDLKSHPEFKMPFIIKNH 224
Cdd:cd10941  161 PIRAKGGILEFPVSVTKLpgLRLPLAGGGyFRLLPYRLIKALIKRSLRRGGPLVLYFHPWEFDPEQPVPGLPLLRRFRTY 240

                        250
                 ....*....|....*...
gi 302150204 225 SG-HELEQRLDRFIKAMK 241
Cdd:cd10941  241 VGlGKAEEKLERLLEDFK 258

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 302150204   1 MILLSFDteefDVPREhgvdfsleegmkvsieGTNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVD 80
Cdd:COG0726   21 AVALTFD----DGPRE----------------GTPRLLDLLKKYGVKATFFVVGSAVERHPELVREIAAAGHEIGNHTYT 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 302150204  81 HWQPKP-------EDVFRSKEIIERVTGVKVAGYRQP--RMFPVSDEDIEKAGYLY 127
Cdd:COG0726   81 HPDLTKlseeeerAEIARAKEALEELTGKRPRGFRPPygRYSPETLDLLAELGYRY 136

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204  26 GMKVsieGTNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVDHWQPKP------EDVF-RSKEIIER 98
Cdd:cd10938   34 GARV---GVPRLLDLLDRYDVKATFFVPGHTAETFPEAVEAILAAGHEIGHHGYLHENPTGltpeeeRELLeRGLELLEK 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204  99 VTGVKVAGYRQP--RMFPVSDEDIEKAGYLYNSSLNPAFIPGRYMHLTTPRtwfmqgKVMQIPASVS----PHlriplfW 172
Cdd:cd10938  111 LTGKRPVGYRSPswEFSPNTLDLLLEHGFLYDSSLMGDDRPYYYVRRGEET------GLVEIPVHWElddfPY------F 178

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 302150204 173 LSMHNFPEWFYLRLVRQVL-----------RHDGYFVTYFHPW 204
Cdd:cd10938  179 AFNRSPPGPPGIAPPRDVLdnwkdefdgayEEGGVFTLTLHPQ 221

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 302150204  32 EGTNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVDH---WQPKP----EDVFRSKEIIERVTGVKV 104
Cdd:cd10959   14 EYTPALLDLLARHGAKATFFVVGERAERHPDLIRRIVDEGHEIGNHGYRHrhpWLRSPwkaiRDLRRAARIIEQLTGRPP 93

                 ....*.
gi 302150204 105 AGYRQP 110
Cdd:cd10959   94 RYYRPP 99

Putative catalytic domain of uncharacterized bacterial polysaccharide deacetylases similar to bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA); This family contains many uncharacterized bacterial 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 302150204  36 RILDILKANNVCATFFCTGNFAELAPEV--MERIKNEGHEVACHGVDH--W---QPKPE---DVFRSKEIIERVTGVKVA 105
Cdd:cd10940   36 RFLDVLDELGLTITVFVVGRDLARDENAkaLRAIADAGHEIANHSFAHdpWlhrYSREEierEIARAEAAILSATGQRPR 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204 106 GYRQPRmFPVSDEDIE---KAGYLYNSSLNPAFI--------------PGRYMHLTTPR--------------TWFMQG- 153
Cdd:cd10940  116 GFRGPG-YSVSADLLEvlaARGYAYDASTFPTFLgplarayylgtaklSGEEKEKRKRLfggfarglrplgapQWRHGSv 194

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204 154 KVMQIPASVSPHLRIPL---FWLSMHNFPE---WFYLRLVRQVLRHDGYFVTY-FHPWEFYD------LKSHPEFKMPfi 220
Cdd:cd10940  195 KLVELPVTTMPLLRLPIhgsYLLYLAQFSLtlaRLYFRTALRLCKVTGVSPSLlLHPTDFLGaeddpsMGFFPGMVLP-- 272

                        250       260
                 ....*....|....*....|....*..
gi 302150204 221 iknhsgheLEQRLDRFIKAMKADKQEF 247
Cdd:cd10940  273 --------QERKRAFATEVLGRLRRHF 291

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 302150204  36 RILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVDHwqPKP---------EDVFRSKEIIERVTGVKVAG 106
Cdd:cd10950   23 AMLTILEKHDVKATFFLEGRWAKKNPDLVRKIAKDGHEIGNHGYSH--PDPsqlsyeqnrEEIRKTNEIIEEITGEKPKL 100

                 ....
gi 302150204 107 YRQP 110
Cdd:cd10950  101 FAPP 104

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 302150204  34 TNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVDHwqpkPEDVFRSKE-IIERVTGV-----KVAGY 107
Cdd:cd10948   55 TPKILDVLKKNDVKATFFVTGHYVKSNPDLIKRMVDEGHIIGNHTVHH----PDMTTLSDEkFKKEITGVeeeykEVTGK 130

                 ....*.
gi 302150204 108 RQPRMF 113
Cdd:cd10948  131 EMMKYF 136

Putative catalytic NodB homology domain of Bacillus subtilis putative polysaccharide deacetylase PdaB, 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 the putative polysaccharide deacetylase PdaB encoded by the pdaB gene on sporulation of Bacillus subtilis. Although its biochemical properties remain to be determined, the PdaB (YbaN) protein is essential for maintaining spores after the late stage of sporulation and is highly conserved in spore-forming bacteria. The glycans of the spore cortex may be candidate PdaB substrates. Based on sequence similarity, the family members are classified as carbohydrate esterase 4 (CE4) superfamily members. However, the classical His-His-Asp zinc-binding motif of CE4 esterases is missing in this family.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204  37 ILDILKAN-NVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVDHW----QPKPE---DVFRSKEIIERVTGVKVAGYR 108
Cdd:cd10949   22 ILDTLKKNgNKKATFFISGPWAERHPELVKRIVADGHEIGSHGYRYKnysdYEDEEikkDLLRAQQAIEKVTGVKPTLLR 101

                 ..
gi 302150204 109 QP 110
Cdd:cd10949  102 PP 103

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 302150204  36 RILDILKANNVCATFFCTGNFAE----LAPEVMERIKNEGHEVACHGVDHwqPKP---------EDVFRSKEIIERVTGV 102
Cdd:cd10967   16 RAAPLLAKYGLKGTFFVNSGLLGrrgyLDLEELRELAAAGHEIGSHTVTH--PDLtslppaelrREIAESRAALEEIGGF 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204 103 KVAGYRQP-RMFPVSDEDIEKAGYLYnsslnpafipGRymHLTTPRTWFMQGKVMQIPASVSPHLRIPLFWLSMHNFPEW 181
Cdd:cd10967   94 PVTSFAYPfGSTNPSIVPLLARGFIA----------AR--GVGGGGNPPNPSDPPADPADCHNADSLALGGPELLLAPDL 161

                        170       180       190
                 ....*....|....*....|....*....|
gi 302150204 182 fylrlVRQVLRHDGYFVTYFHPWEFYDLKS 211
Cdd:cd10967  162 -----LDAAKKNGGWLVLWGHSVEGDGTKY 186

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 302150204  33 GTNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHG 78
Cdd:cd10958   14 STEEILDLLEEHNVRATFFVIGSHAPRREEVLSRIVEEGHELGNHG 59

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204   1 MILLSFDteefDVPREhgvdfsleegmkvsiEGTNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVD 80
Cdd:cd10954    2 MVALTFD----DGPNA---------------KYTPRLLDVLEKYNVRATFFLVGQNVNGNKEIVKRMVEMGCEIGNHSYT 62

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 302150204  81 HWQ---PKPEDV----FRSKEIIERVTGVKVAGYRQP 110
Cdd:cd10954   63 HPDltkLSPSEIkkeiEKTNEAIKKITGKRPKLFRPP 99

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 302150204  26 GMKVsieGTNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVD-----HWQPKP---EDVFRSKEIIE 97
Cdd:cd10979   60 GNRV---GIWRLLDALDELGIPPTVALNAAVADRYPELIEAIRERGWEFIAHGISnstlhAGLDEAqerEVIAESLDRIE 136

                         90
                 ....*....|...
gi 302150204  98 RVTGVKVAGYRQP 110
Cdd:cd10979  137 KATGQRPRGWLSP 149

Putative catalytic domain of rhizobial NodB chitooligosaccharide N-deacetylase and its bacterial homologs; This family corresponds to rhizobial NodB chitooligosaccharide N-deacetylase (EC 3.5.1.-), encoded by nodB gene from the nodulation (nod) gene cluster that is responsible for the biosynthesis of bacterial nodulation signals, termed Nod factors. NodB is involved in de-N-acetylating the nonreducing N-acetylglucosamine residue of chitooligosaccharides to allow for the attachment of the fatty acyl group by the acyltransferase NodA. The monosaccharide N-acetylglucosamine cannot be deacetylated by NodB. NodB is composed of a 6-stranded barrel catalytic domain with detectable sequence similarity to the 7-stranded barrel homology domain of polysaccharide deacetylase (DCA)-like proteins in the larger carbohydrate esterase 4 (CE4) superfamily.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 302150204  34 TNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVDH 81
Cdd:cd10943   16 TPQVLDVLAEHRVPATFFVIGAYAAEHPELIRRMIAEGHEVGNHTMTH 63

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204  34 TNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHGVDHwqPKPEDVFRSK---------EIIERVTGVKV 104
Cdd:cd10947   16 TPQVLKTLKKYKAPATFFMLGSNVKTYPELVRRVLDAGHEIGNHSWSH--PQLTKLSVAEaekqindtdDAIEKATGNRP 93

                 ....*.
gi 302150204 105 AGYRQP 110
Cdd:cd10947   94 TLLRPP 99

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204  42 KANNVC---ATFFCTGNFAElaPEVMERIKNEGHEVACHGVDH------WQPKP--EDVFRSKEIIER---VTGVKVAGY 107
Cdd:cd10919   29 NNNGGCpipATFFVSTNYTD--CSLVKQLWREGHEIATHTVTHvpddsnASVDEweEEIAGQREWLNKtcgIPLEKVVGF 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 302150204 108 RQPRMfpVSDED----IEKAGYLYNSSlnpafIPGRYMHLTTPRTW--FMQGKVMQI----PASVSPHLRIPLFW 172
Cdd:cd10919  107 RAPYL--AYNPNtrevLEENGFLYDSS-----IPEPYTPSGTNRLWpyTLDYGIPQDcnlvPGSCSPTERYPGLW 174

Domain of unknown function (DUF3473); This presumed domain is functionally uncharacterized. This domain is found in bacteria and archaea. This domain is about 130 amino acids in length. This domain is found associated with pfam01522. This domain has two completely conserved residues (P and H) that may be functionally important.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204  152 QGKVMQIPASVSP--HLRIPL---FWLSMhnFPEWFYLRLVRQVLRHDGYFVTYFHPWEF 206
Cdd:pfam11959  27 GGSLVEFPVSTLRlgGRNLPLgggGYFRL--FPYPLSRWAIRRVNREGRPAVFYFHPWEI 84

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204  40 ILKANNVCATFFCTGNFAELAPEV---------------MERIKNEGHEVACHGVDHwqPKP---------EDVFRSKEI 95
Cdd:cd10918   20 ILKKYGLPATFFVITGYIGGGNPWwapapprppyltwdqLRELAASGVEIGSHTHTH--PDLttlsdeelrRELAESKER 97

                 ....*....
gi 302150204  96 IERVTGVKV 104
Cdd:cd10918   98 LEEELGKPV 106

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 302150204  62 EVMERIKNEGHEVACHGVDHWQPKPEDVFRSKEIIERVTGVKVAGYRQPR-MFPVSD--EDIEKAGYLYNSSL----NPA 134
Cdd:cd10931   56 SLIKEIADRGWEIGLHGSYNSYTDPEKLKKEKERLEKILGRPVTGGRQHYlRFDLPEtwRNLADAGFTYDSTMgyadVAG 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302150204 135 FIPGRymhlTTPRTWFMqgkvmqIPASVSPHLRI-PLFWLS-------MHNFPE-WFYL-RLVRQVLRHDGYFVTYFHPW 204
Cdd:cd10931  136 FRAGT----CFPFRFYD------LNTERQLPLLEhPLVIMDctlfgykYMNPEEaLEEIkQLIDEVKKVGGVFTLLWHNS 205

                 ....
gi 302150204 205 EFYD 208
Cdd:cd10931  206 SFSE 209

Putative catalytic domain of Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; This family is represented by Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), encoded by the cda1 gene. 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 be involved in allantoin hydrolysis. It is likely an ortholog to bacterial 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 302150204  15 REHGVDFSLEEGMKVsieGTNRILDILKANNVCATFFCTGNFAELAPEVMERIKNEGHEVACHG 78
Cdd:cd10980   48 RDVSIESLYEYGSRC---GFWRILRLFKKHGVKFTCFAVGQALEKNPAVAGAMEEGGHEVASHG 108