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Conserved domains on  [gi|1332788139|ref|WP_102770248|]
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MULTISPECIES: polysaccharide deacetylase family protein [Paucibacter]

Protein Classification

polysaccharide deacetylase family protein( domain architecture ID 10180925)

polysaccharide deacetylase family protein belonging to the carbohydrate esterase 4 (CE4) superfamily, may catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan; similar to Bacillus subtilis polysaccharide deacetylase YxkH

CATH:  3.20.20.370
CAZY:  CE4
EC:  3.-.-.-
Gene Ontology:  GO:0005975|GO:0046872|GO:0016787
PubMed:  12644381
SCOP:  3001025

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CE4_NodB_like_5s_6s cd10918
Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a ...
76-298 1.46e-50

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: 164.69  E-value: 1.46e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  76 ACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFLGQGRMWNDRiieairhapagaldlstvtgdersrfqigdassr 155
Cdd:cd10918     1 PVVLTFDDGYRDNYTYALPILKKYGLPATFFVITGYIGGGNPWWAP---------------------------------- 46
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 156 rqaidallgvikyrvpdervqcvaaietlcggAHDQALMMGDAGIRQLRAAGMQIGAHTVNHPILATLDAAGMRREIGDS 235
Cdd:cd10918    47 --------------------------------APPRPPYLTWDQLRELAASGVEIGSHTHTHPDLTTLSDEELRRELAES 94
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1332788139 236 KDYLEAVLREPVRLFAYPNGkpgqDYNADSVAQVKDLGFLAAVSTVWGAARQGDSMFELPRFT 298
Cdd:cd10918    95 KERLEEELGKPVRSFAYPYG----RYNPRVIAALKEAGYKAAFTTDPGLNSPGDDPYALPRIN 153
CE4_SF super family cl15692
Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate ...
18-112 1.41e-11

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.


The actual alignment was detected with superfamily member TIGR03938:

Pssm-ID: 472828  Cd Length: 619  Bit Score: 65.03  E-value: 1.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  18 RLTILTLHRVLP-QADDIFPGEVDAARFREILGWL--NDWaHVMPLD--EAAERlARGSLPARACVLTFDDGYEDNVSVA 92
Cdd:TIGR03938   2 TFVVLCYHDVRDdSAADQDPYAVSTDALIEHFNWLrqNGY-HPVSVDqiLDARR-GGKPLPEKAVLLTFDDGYRSFYTRV 79
                          90       100
                  ....*....|....*....|
gi 1332788139  93 LPILQEFRMPATFFIATGFL 112
Cdd:TIGR03938  80 FPLLKAYNYPAVLALVGSWL 99
 
Name Accession Description Interval E-value
CE4_NodB_like_5s_6s cd10918
Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a ...
76-298 1.46e-50

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: 164.69  E-value: 1.46e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  76 ACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFLGQGRMWNDRiieairhapagaldlstvtgdersrfqigdassr 155
Cdd:cd10918     1 PVVLTFDDGYRDNYTYALPILKKYGLPATFFVITGYIGGGNPWWAP---------------------------------- 46
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 156 rqaidallgvikyrvpdervqcvaaietlcggAHDQALMMGDAGIRQLRAAGMQIGAHTVNHPILATLDAAGMRREIGDS 235
Cdd:cd10918    47 --------------------------------APPRPPYLTWDQLRELAASGVEIGSHTHTHPDLTTLSDEELRRELAES 94
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1332788139 236 KDYLEAVLREPVRLFAYPNGkpgqDYNADSVAQVKDLGFLAAVSTVWGAARQGDSMFELPRFT 298
Cdd:cd10918    95 KERLEEELGKPVRSFAYPYG----RYNPRVIAALKEAGYKAAFTTDPGLNSPGDDPYALPRIN 153
CDA1 COG0726
Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ...
57-282 9.40e-29

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: 109.36  E-value: 9.40e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  57 VMPLDEAAERLARGSLPARACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFLGqgrmwndriieairhapagaldl 136
Cdd:COG0726     2 VLSLDELLPALRWGPLPKKAVALTFDDGPREGTPRLLDLLKKYGVKATFFVVGSAVE----------------------- 58
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 137 stvtgdersrfqigdassrrqaidallgvikyRVPDErvqcvaaietlcggahdqalmmgdagIRQLRAAGMQIGAHTVN 216
Cdd:COG0726    59 --------------------------------RHPEL--------------------------VREIAAAGHEIGNHTYT 80
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1332788139 217 HPILATLDAAGMRREIGDSKDYLEAVLREPVRLFAYPNGkpgqDYNADSVAQVKDLGFLAAVSTVW 282
Cdd:COG0726    81 HPDLTKLSEEEERAEIARAKEALEELTGKRPRGFRPPYG----RYSPETLDLLAELGYRYILWDSV 142
Polysacc_deac_1 pfam01522
Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of ...
69-277 8.00e-23

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: 91.52  E-value: 8.00e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  69 RGSLPARACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFLGQGrmwndriieairhapagaldlstvtgdersrfq 148
Cdd:pfam01522   1 KGPTPKKVVALTFDDGPSENTPAILDVLKKYGVKATFFVIGGNVERY--------------------------------- 47
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 149 igdassrrqaidallgvikyrvPDErvqcvaaietlcggahdqalmmgdagIRQLRAAGMQIGAHTVNHPILATLDAAGM 228
Cdd:pfam01522  48 ----------------------PDL--------------------------VKRMVEAGHEIGNHTWSHPNLTGLSPEEI 79
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1332788139 229 RREIGDSKDYLEAVLREPVRLFAYPNGkpgqDYNADSVAQVKDLGFLAA 277
Cdd:pfam01522  80 RKEIERAQDALEKATGKRPRLFRPPYG----SYNDTVLEVAKKLGYTAV 124
deacetyl_PgaB TIGR03938
poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB; Two well-characterized systems ...
18-112 1.41e-11

poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB; Two well-characterized systems produce polysaccharide based on N-acetyl-D-glucosamine in straight chains with beta-1,6 linkages. These are encoded by the icaADBC operon in Staphylococcus species, where the system is designated polysaccharide intercellular adhesin (PIA), and the pgaABCD operon in Gram-negative bacteria such as E. coli. Both systems include a putative polysaccharide deacetylase. The PgaB protein, described here, contains an additional domain lacking from its Gram-positive counterpart IcaB (TIGR03933). Deacetylation by this protein appears necessary to allow export through the porin PgaA [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]


Pssm-ID: 274867  Cd Length: 619  Bit Score: 65.03  E-value: 1.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  18 RLTILTLHRVLP-QADDIFPGEVDAARFREILGWL--NDWaHVMPLD--EAAERlARGSLPARACVLTFDDGYEDNVSVA 92
Cdd:TIGR03938   2 TFVVLCYHDVRDdSAADQDPYAVSTDALIEHFNWLrqNGY-HPVSVDqiLDARR-GGKPLPEKAVLLTFDDGYRSFYTRV 79
                          90       100
                  ....*....|....*....|
gi 1332788139  93 LPILQEFRMPATFFIATGFL 112
Cdd:TIGR03938  80 FPLLKAYNYPAVLALVGSWL 99
pgaB PRK14582
poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB;
39-103 1.57e-04

poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB;


Pssm-ID: 184754 [Multi-domain]  Cd Length: 671  Bit Score: 43.22  E-value: 1.57e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1332788139  39 VDAARFREILGWL--NDWAHVMPLDEAAERLARGSLPARACVLTFDDGYEDNVSVALPILQEFRMPA 103
Cdd:PRK14582   69 VRTSALREQFAWLreNGYQPVSVAQILEAHRGGKPLPEKAVLLTFDDGYSSFYTRVFPILQAFQWPA 135
 
Name Accession Description Interval E-value
CE4_NodB_like_5s_6s cd10918
Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a ...
76-298 1.46e-50

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: 164.69  E-value: 1.46e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  76 ACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFLGQGRMWNDRiieairhapagaldlstvtgdersrfqigdassr 155
Cdd:cd10918     1 PVVLTFDDGYRDNYTYALPILKKYGLPATFFVITGYIGGGNPWWAP---------------------------------- 46
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 156 rqaidallgvikyrvpdervqcvaaietlcggAHDQALMMGDAGIRQLRAAGMQIGAHTVNHPILATLDAAGMRREIGDS 235
Cdd:cd10918    47 --------------------------------APPRPPYLTWDQLRELAASGVEIGSHTHTHPDLTTLSDEELRRELAES 94
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1332788139 236 KDYLEAVLREPVRLFAYPNGkpgqDYNADSVAQVKDLGFLAAVSTVWGAARQGDSMFELPRFT 298
Cdd:cd10918    95 KERLEEELGKPVRSFAYPYG----RYNPRVIAALKEAGYKAAFTTDPGLNSPGDDPYALPRIN 153
CE4_Ecf1_like_5s cd10969
Putative catalytic NodB homology domain of a hypothetical protein Ecf1 from Escherichia coli ...
44-311 5.56e-32

Putative catalytic NodB homology domain of a hypothetical protein Ecf1 from Escherichia coli and similar proteins; This family contains a hypothetical protein Ecf1 from Escherichia coli and its prokaryotic homologs. Although their biochemical properties remain to be determined, members in this family contain a conserved domain with a 5-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: 213026 [Multi-domain]  Cd Length: 218  Bit Score: 118.54  E-value: 5.56e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  44 FREILGWL--NDWaHVMPLDEAAERLARGS-LPARACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFlgqgrmwnd 120
Cdd:cd10969     4 FEEQLKYLkkNGY-RTLSLEELLAFLKGGKpLPKKSVLITFDDGYLDNYVYAYPILKKYGLKATIFVVTGF--------- 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 121 riieairhapagaldlstvtgdersrfqIGDASSRRQAIDallgvikyrvpDERVQCVAAIETLCGGAHDQALMMGDAGI 200
Cdd:cd10969    74 ----------------------------IDEASGVRPTLF-----------DYWSGDMPEANKIFFLKGRDEVFLSWEEL 114
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 201 RQLRAAG-MQIGAHTVNHpilatldaAGMRREIGDSKDYLEAVLREPVRLFAYPNGkpgqDYNADSVAQVKDLGFLAAVS 279
Cdd:cd10969   115 REMEDSGvFDIQSHSHSH--------TRVEYELEESKRLLEENLGKKVDHFCWPWG----HYSPESLRIAKELGFKFFFT 182
                         250       260       270
                  ....*....|....*....|....*....|..
gi 1332788139 280 TVWGAARQGDSMFELPRFTPWDTSRFRYRSRI 311
Cdd:cd10969   183 TKKGVNVPGEDPDRIKRITVKKDGGFWLKKRL 214
CE4_Mlr8448_like_5s cd10968
Putative catalytic NodB homology domain of Mesorhizobium loti Mlr8448 protein and its ...
75-298 3.34e-29

Putative catalytic NodB homology domain of Mesorhizobium loti Mlr8448 protein and its bacterial homologs; This family contains Mesorhizobium loti Mlr8448 protein and its bacterial homologs. Although their biochemical properties are yet to be determined, members in this subfamily contain a conserved domain with a 5-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: 213025 [Multi-domain]  Cd Length: 161  Bit Score: 109.65  E-value: 3.34e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  75 RACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFL-GQGRMWNDriieairhapagaldlstvtgdersrfqigdas 153
Cdd:cd10968     1 RFAVLTFDDGYRDNLEFALPVFERHGVPFTIYVTTGFPdGTGELWWL--------------------------------- 47
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 154 srrqaidallgvikyrvpdervqcvaAIEtlcggahdqalMMGDAGIRQLRAAGM-QIGAHTVNHPILATLDAAGMRREI 232
Cdd:cd10968    48 --------------------------TLE-----------CLDWDELRRLAADPLvTIGAHTITHPNLARLSDDEARREI 90
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1332788139 233 GDSKDYLEAVLREPVRLFAYPNGKPGqDYNADSVAQVKDLGFLAAVSTVWGA--ARQGDSMFELPRFT 298
Cdd:cd10968    91 AASRARLEAELGREVRHFAYPYGDRT-AAGPREADLAREAGFATAVTTRPGVlfAEHRENLHALPRIS 157
CDA1 COG0726
Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ...
57-282 9.40e-29

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: 109.36  E-value: 9.40e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  57 VMPLDEAAERLARGSLPARACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFLGqgrmwndriieairhapagaldl 136
Cdd:COG0726     2 VLSLDELLPALRWGPLPKKAVALTFDDGPREGTPRLLDLLKKYGVKATFFVVGSAVE----------------------- 58
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 137 stvtgdersrfqigdassrrqaidallgvikyRVPDErvqcvaaietlcggahdqalmmgdagIRQLRAAGMQIGAHTVN 216
Cdd:COG0726    59 --------------------------------RHPEL--------------------------VREIAAAGHEIGNHTYT 80
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1332788139 217 HPILATLDAAGMRREIGDSKDYLEAVLREPVRLFAYPNGkpgqDYNADSVAQVKDLGFLAAVSTVW 282
Cdd:COG0726    81 HPDLTKLSEEEERAEIARAKEALEELTGKRPRGFRPPYG----RYSPETLDLLAELGYRYILWDSV 142
CE4_DAC_u2_5s cd10971
Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide ...
76-305 1.18e-23

Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; This family contains many uncharacterized prokaryotic polysaccharide deacetylases. Although their biological functions remain unknown, all members of this family are predicted to contain a conserved domain with a 5-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: 200593 [Multi-domain]  Cd Length: 198  Bit Score: 95.84  E-value: 1.18e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  76 ACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFLGQGRMWNDRIIEAIRhapagaldlstvtgdERSR-FQIG-DAS 153
Cdd:cd10971     1 AILLTFDDGYKDHYTYVLPELEERGIQGSFFVPAKPVEEHKVLDVNKIHFIL---------------FIKRlLQYElPEK 65
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 154 SRRQAIDALLGVIKYrVPDErvqcvaaietlcggAHDQALMMGDAGIRQLRAAGMQIGAHTVNHPILATLDAAGMRREIG 233
Cdd:cd10971    66 LRTEILDKLFKKYVD-ISEE--------------AFAKELYMTKDQIKQLERAGMHIGSHGYDHYWLGRLSPEEQEAEIK 130
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1332788139 234 DSKDYLEAVLREPVRL-FAYPNGkpgqDYNADSVAQVKDLGFLAAVSTVWGAARQGD-SMFELPRftpWDTSRF 305
Cdd:cd10971   131 KSLKFLSEVGGGHDRWtFCYPYG----SFNEETLEILKENGCRLGFTTEVAIADLDDlEPLELPR---YDCNDF 197
Polysacc_deac_1 pfam01522
Polysaccharide deacetylase; This domain is found in polysaccharide deacetylase. This family of ...
69-277 8.00e-23

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: 91.52  E-value: 8.00e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  69 RGSLPARACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFLGQGrmwndriieairhapagaldlstvtgdersrfq 148
Cdd:pfam01522   1 KGPTPKKVVALTFDDGPSENTPAILDVLKKYGVKATFFVIGGNVERY--------------------------------- 47
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 149 igdassrrqaidallgvikyrvPDErvqcvaaietlcggahdqalmmgdagIRQLRAAGMQIGAHTVNHPILATLDAAGM 228
Cdd:pfam01522  48 ----------------------PDL--------------------------VKRMVEAGHEIGNHTWSHPNLTGLSPEEI 79
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1332788139 229 RREIGDSKDYLEAVLREPVRLFAYPNGkpgqDYNADSVAQVKDLGFLAA 277
Cdd:pfam01522  80 RKEIERAQDALEKATGKRPRLFRPPYG----SYNDTVLEVAKKLGYTAV 124
CE4_DAC_u4_5s cd10973
Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide ...
75-297 4.78e-20

Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; This family contains many uncharacterized bacterial polysaccharide deacetylases. Although their biological functions remain unknown, all members of the family are predicted to contain a conserved domain with a 5-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: 213028 [Multi-domain]  Cd Length: 157  Bit Score: 85.02  E-value: 4.78e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  75 RACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFLGQGRMwndriieairhapagaldlstvtgdersrfqigdass 154
Cdd:cd10973     1 KTVVITIDDGYKSVYTNAFPILKKYGYPFTLFVYTEAIGRGYP------------------------------------- 43
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 155 rrqaidallgvikyrvpdervqcvaaietlcggahdqaLMMGDAGIRQLRAAGMQIGAHTVNHPILATL-------DAAG 227
Cdd:cd10973    44 --------------------------------------DYLSWDQIREMAKYGVEIANHSYSHPHLVRLgekmqeqWLEW 85
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 228 MRREIGDSKDYLEAVLREPVRLFAYPNGkpgqDYNADSVAQVKDLGFLAAVSTVWGAARQGDSMFELPRF 297
Cdd:cd10973    86 IRQDIEKSQQRFEKELGKKPKLFAYPYG----EYNPAIIKLVKEAGFEAAFQQSGGVVSAGTDLTALPRF 151
CE4_GLA_like_6s cd10967
Putative catalytic NodB homology domain of gellan lyase and similar proteins; This family is ...
78-292 5.80e-18

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: 80.50  E-value: 5.80e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  78 VLTFDDGYEDNVSVAlPILQEFRMPATFFIATGFLGQGRMWNdriieairhapagaldlstvtgdersrfqigdassrrq 157
Cdd:cd10967     4 SLTFDDGYAQDLRAA-PLLAKYGLKGTFFVNSGLLGRRGYLD-------------------------------------- 44
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 158 aidallgvikyrvPDErvqcvaaietlcggahdqalmmgdagIRQLRAAGMQIGAHTVNHPILATLDAAGMRREIGDSKD 237
Cdd:cd10967    45 -------------LEE--------------------------LRELAAAGHEIGSHTVTHPDLTSLPPAELRREIAESRA 85
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1332788139 238 YLEAVLREPVRLFAYPNGkpgqDYNaDSVAQVKDLGFLAAVSTVWGAARQGDSMF 292
Cdd:cd10967    86 ALEEIGGFPVTSFAYPFG----STN-PSIVPLLARGFIAARGVGGGGNPPNPSDP 135
CE4_yadE_5s cd10966
Putative catalytic polysaccharide deacetylase domain of uncharacterized protein yadE and ...
73-298 3.19e-14

Putative catalytic polysaccharide deacetylase domain of uncharacterized protein yadE and similar proteins; This family contains an uncharacterized protein yadE from Escherichia coli and its bacterial homologs. Although its molecular function remains unknown, yadE shows high sequence similarity with the catalytic NodB homology domain of outer membrane lipoprotein PgaB and the surface-attached protein intercellular adhesion protein IcaB. Both PgaB and IcaB are essential in bacterial biofilm formation.


Pssm-ID: 213024 [Multi-domain]  Cd Length: 164  Bit Score: 69.23  E-value: 3.19e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  73 PARACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFLGQgrmwndriieairhAPAGALDLSTVTGDErsrfqigda 152
Cdd:cd10966     1 PEKSVVITFDDGYKSNYEYAYPILKKYGFKATIFVIGSRIGE--------------KPQDPKILQYLSIEE--------- 57
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 153 ssrrqaIDALLGVIKYrvpdervqcvaaietlcgGAHD----QALMMGDAGIRQLRaagmqigahtvNHPILATLDAAgm 228
Cdd:cd10966    58 ------LKEMRDVFEF------------------QSHTynmhRGGGTGGHGLLALS-----------EEEILADLKKS-- 100
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 229 rREIGDSKDYleavlrepvrlFAYPNGkpgqDYNADSVAQVKDLGFLAAVSTVWGAARQGDSMFELPRFT 298
Cdd:cd10966   101 -EEILGSSKA-----------FAYPYG----DYNDNAIEALKEAGVKLAFTTNEGKVTPGDDPYELPRVR 154
CE4_DAC_u1_6s cd10970
Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide ...
76-298 1.05e-13

Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide deacetylases which consist of a 6-stranded beta/alpha barrel; This family contains uncharacterized prokaryotic polysaccharide deacetylases. 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: 213027 [Multi-domain]  Cd Length: 194  Bit Score: 68.50  E-value: 1.05e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  76 ACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFLGQ-GRMwndriieairhapagaldlstvtgdersrfqigdasS 154
Cdd:cd10970     2 KVSLTFDDGYESQYTTAFPILQEYGIPATAAVIPDSIGSsGRL------------------------------------T 45
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 155 RRQaidallgvikyrvpdervqcvaaietlcggahdqalmmgdagIRQLRAAGMQIGAHTVNHPILATLDAAGMRREIGD 234
Cdd:cd10970    46 LDQ------------------------------------------LRELQDAGWEIASHTLTHTDLTELSADEQRAELTE 83
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1332788139 235 SKDYLEAVLREP-VRLFAYPNGkpgqDYNADSVAQVKDLGFLAAVSTVWGAARQGDSMFELPRFT 298
Cdd:cd10970    84 SKRWLEDNGFGDgADHFAYPYG----RYDDEVLELVREYYDLGRSGGGGPNGRPPLDPYRLRRVT 144
deacetyl_PgaB TIGR03938
poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB; Two well-characterized systems ...
18-112 1.41e-11

poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB; Two well-characterized systems produce polysaccharide based on N-acetyl-D-glucosamine in straight chains with beta-1,6 linkages. These are encoded by the icaADBC operon in Staphylococcus species, where the system is designated polysaccharide intercellular adhesin (PIA), and the pgaABCD operon in Gram-negative bacteria such as E. coli. Both systems include a putative polysaccharide deacetylase. The PgaB protein, described here, contains an additional domain lacking from its Gram-positive counterpart IcaB (TIGR03933). Deacetylation by this protein appears necessary to allow export through the porin PgaA [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]


Pssm-ID: 274867  Cd Length: 619  Bit Score: 65.03  E-value: 1.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  18 RLTILTLHRVLP-QADDIFPGEVDAARFREILGWL--NDWaHVMPLD--EAAERlARGSLPARACVLTFDDGYEDNVSVA 92
Cdd:TIGR03938   2 TFVVLCYHDVRDdSAADQDPYAVSTDALIEHFNWLrqNGY-HPVSVDqiLDARR-GGKPLPEKAVLLTFDDGYRSFYTRV 79
                          90       100
                  ....*....|....*....|
gi 1332788139  93 LPILQEFRMPATFFIATGFL 112
Cdd:TIGR03938  80 FPLLKAYNYPAVLALVGSWL 99
CE4_NodB_like_6s_7s cd10917
Catalytic NodB homology domain of rhizobial NodB-like proteins; This family belongs to the ...
200-273 1.42e-09

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: 56.09  E-value: 1.42e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1332788139 200 IRQLRAAGMQIGAHTVNHPILATLDAAGMRREIGDSKDYLEAVLREPVRLFAYPNGkpgqDYNADSVAQVKDLG 273
Cdd:cd10917    46 VRRIVAEGHEIGNHTYSHPDLTKLSPEEIRAEIERTQDAIEEATGVRPRLFRPPYG----AYNPEVLAAAAELG 115
CE4_BsYlxY_like cd10950
Putative catalytic NodB homology domain of uncharacterized protein YlxY from Bacillus subtilis ...
201-273 2.64e-08

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: 53.05  E-value: 2.64e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1332788139 201 RQLRAAGMQIGAHTVNHPILATLDAAGMRREIGDSKDYLEAVLREPVRLFAYPNGkpgqDYNADSVAQVKDLG 273
Cdd:cd10950    52 RKIAKDGHEIGNHGYSHPDPSQLSYEQNREEIRKTNEIIEEITGEKPKLFAPPYG----EFNDAVVKAAAELG 120
CE4_PgaB_5s cd10964
N-terminal putative catalytic polysaccharide deacetylase domain of bacterial poly-beta-1, ...
72-112 1.19e-07

N-terminal putative catalytic polysaccharide deacetylase domain of bacterial poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, and similar proteins; This family is represented by an outer membrane lipoprotein, poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase (PgaB, EC 3.5.1.-), encoded by Escherichia coli pgaB gene from the pgaABCD (formerly ycdSRQP) operon, which affects biofilm development by promoting abiotic surface binding and intercellular adhesion. PgaB catalyzes the N-deacetylation of poly-beta-1,6-N-acetyl-D-glucosamine (PGA), a biofilm adhesin polysaccharide that stabilizes biofilms of E. coli and other bacteria. PgaB contains an N-terminal NodB homology domain with a 5-stranded beta/alpha barrel, and a C-terminal carbohydrate binding domain required for PGA N-deacetylation, which may be involved in binding to unmodified poly-beta-1,6-GlcNAc and assisting catalysis by the deacetylase domain. This family also includes several orthologs of PgaB, such as the hemin storage system HmsF protein, encoded by Yersinia pestis hmsF gene from the hmsHFRS operon, which is essential for Y. pestis biofilm formation. Like PgaB, HmsF is an outer membrane protein with an N-terminal NodB homology domain, which is likely involved in the modification of the exopolysaccharide (EPS) component of the biofilm. HmsF also has a conserved but uncharacterized C-terminal domain that is present in other HmsF-like proteins in Gram-negative bacteria. This alignment model corresponds to the N-terminal NodB homology domain.


Pssm-ID: 200586 [Multi-domain]  Cd Length: 193  Bit Score: 51.19  E-value: 1.19e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1332788139  72 LPARACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFL 112
Cdd:cd10964     1 LPAKAVLLTFDDGYQSFYTRVYPLLKAYKYPAVLALVGSWL 41
CE4_CtAXE_like cd10954
Catalytic NodB homology domain of Clostridium thermocellum acetylxylan esterase and its ...
200-274 7.37e-07

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: 48.74  E-value: 7.37e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1332788139 200 IRQLRAAGMQIGAHTVNHPILATLDAAGMRREIGDSKDYLEAVLREPVRLFAYPNGkpgqDYNaDSVAQVKDLGF 274
Cdd:cd10954    46 VKRMVEMGCEIGNHSYTHPDLTKLSPSEIKKEIEKTNEAIKKITGKRPKLFRPPYG----AVN-DTVKKAIDLPF 115
CE4_BH0857_like cd10955
Putative catalytic NodB homology domain of uncharacterized BH0857 protein from Bacillus ...
197-277 4.11e-06

Putative catalytic NodB homology domain of uncharacterized BH0857 protein from Bacillus halodurans and its bacterial homologs; This family is represented by a putative polysaccharide deacetylase BH0857 from Bacillus halodurans. Although its biological function still remains unknown, BH0857 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 BH0857 and SpPgdA belong to the carbohydrate esterase 4 (CE4) superfamily. This family also includes many uncharacterized bacterial polysaccharide deacetylases.


Pssm-ID: 200579 [Multi-domain]  Cd Length: 195  Bit Score: 46.54  E-value: 4.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 197 DAGIRQLRAAGM-QIGAHTVNHP-------ILATLDAAGMRREIGDSKDYLEAVLREPVRLFAYPNGKpgqdYNADSVAQ 268
Cdd:cd10955    46 PAEAKELAANPLfEIENHGYRHPplsvngrIKGTLSVEEVRREIEGNQEAIEKATGRKPRYFRFPTAY----YDEVAVEL 121

                  ....*....
gi 1332788139 269 VKDLGFLAA 277
Cdd:cd10955   122 VEALGYKVV 130
CE4_BsPdaA_like cd10948
Catalytic NodB homology domain of Bacillus subtilis polysaccharide deacetylase PdaA, and its ...
200-274 1.97e-05

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.


Pssm-ID: 200572 [Multi-domain]  Cd Length: 223  Bit Score: 44.97  E-value: 1.97e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1332788139 200 IRQLRAAGMQIGAHTVNHPILATLDAAGMRREIGDSKDYLEAVL-REPVRLFAYPNGKpgqdYNADSVAQVKDLGF 274
Cdd:cd10948    85 IKRMVDEGHIIGNHTVHHPDMTTLSDEKFKKEITGVEEEYKEVTgKEMMKYFRPPRGE----FSERSLKITKDLGY 156
CE4_DAC_u3_5s cd10972
Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide ...
200-306 3.17e-05

Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; This family contains uncharacterized bacterial polysaccharide deacetylases. Although their biological functions remain unknown, all members of the family are predicted to contain a conserved domain with a 5-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: 200594 [Multi-domain]  Cd Length: 216  Bit Score: 44.24  E-value: 3.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 200 IRQLRAAGMQIGAHTVNHPILATLDAAGMRREIGDSKDYL-EAVLREPVRLFAYPNG-KPGQDYNADSVAQVKDLGF-LA 276
Cdd:cd10972    74 LRWLVELGYEIGNHTYTHVNLNKLDAEEIQEELARVNKMIeEAIPGYEVESLALPFGmKPKENRALVLSGEYEGVSYkHQ 153
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1332788139 277 AVSTV-WGAARqgdSMFElPRFTPWDTSRFR 306
Cdd:cd10972   154 AVLLVgAEPAP---SPYS-KDFDPAAIPRIR 180
CE4_SpPgdA_BsYjeA_like cd10947
Catalytic NodB homology domain of Streptococcus pneumoniae peptidoglycan deacetylase PgdA, ...
200-274 4.66e-05

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: 43.14  E-value: 4.66e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1332788139 200 IRQLRAAGMQIGAHTVNHPILATLDAAGMRREIGDSKDYLEAVLREPVRLFAYPngkpgqdYNA--DSVAQVKDLGF 274
Cdd:cd10947    46 VRRVLDAGHEIGNHSWSHPQLTKLSVAEAEKQINDTDDAIEKATGNRPTLLRPP-------YGAtnRSIRQIAGLTI 115
CE4_SF cd10585
Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate ...
200-263 1.00e-04

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: 41.66  E-value: 1.00e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1332788139 200 IRQLRAAGMQIGAHTVNHPILAT--LDAAGMRREIGDSKDYLEAVLREPVRLFAYPNGKPGQDYNA 263
Cdd:cd10585    57 LRELLAYGHEIGLHGYTHPDLAYgnLSPEEVLEDLLRARRILEEAGGQPPKGFRAPGGNLSETVKA 122
pgaB PRK14582
poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB;
39-103 1.57e-04

poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB;


Pssm-ID: 184754 [Multi-domain]  Cd Length: 671  Bit Score: 43.22  E-value: 1.57e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1332788139  39 VDAARFREILGWL--NDWAHVMPLDEAAERLARGSLPARACVLTFDDGYEDNVSVALPILQEFRMPA 103
Cdd:PRK14582   69 VRTSALREQFAWLreNGYQPVSVAQILEAHRGGKPLPEKAVLLTFDDGYSSFYTRVFPILQAFQWPA 135
hmsF PRK14581
outer membrane N-deacetylase; Provisional
21-103 7.27e-04

outer membrane N-deacetylase; Provisional


Pssm-ID: 184753 [Multi-domain]  Cd Length: 672  Bit Score: 41.12  E-value: 7.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139  21 ILTLHRVLPQADDIFPGEVDAARFREILGWLNDWA-HVMPLDEA-AERLARGSLPARACVLTFDDGYEDNVSVALPILQE 98
Cdd:PRK14581   51 VIAYHDVEDDSADQRYLSVRSSALNEQFVWLRDNGyHVVSVDQIlAARNGGPTLPDKAVLLTFDDGYSSFYRRVYPLLKA 130

                  ....*
gi 1332788139  99 FRMPA 103
Cdd:PRK14581  131 YKWSA 135
CE4_IcaB_5s cd10965
Putative catalytic polysaccharide deacetylase domain of bacterial intercellular adhesion ...
73-114 1.03e-03

Putative catalytic polysaccharide deacetylase domain of bacterial intercellular adhesion protein IcaB and similar proteins; The family is represented by the surface-attached protein intercellular adhesion protein IcaB (Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase, EC 3.5.1.-), encoded by Staphylococcus epidermidis icaB gene from the icaABC gene cluster that is involved in the synthesis of polysaccharide intercellular adhesin (PIA), which is located mainly on the cell surface. IcaB is a secreted, cell wall-associated protein that plays a crucial role in exopolysaccharide modification in bacterial biofilm formation. It catalyzes the N-deacetylation of poly-beta-1,6-N-acetyl-D-glucosamine (PNAG, also referred to as PIA), a biofilm adhesin polysaccharide. IcaB shows high homology to the N-terminal NodB homology domain of Escherichia coli PgaB. At this point, they are classified in the same family.


Pssm-ID: 200587 [Multi-domain]  Cd Length: 172  Bit Score: 39.29  E-value: 1.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1332788139  73 PARACVLTFDDGYEDNVSVALPILQEFRMPATFFIATGFLGQ 114
Cdd:cd10965     1 PGKYVVITFDDVDQTVYDNAFPILKKLKIPFTQFVITGQVGS 42
CE4_ClCDA_like cd10951
Catalytic NodB homology domain of Colletotrichum lindemuthianum chitin deacetylase and similar ...
200-273 1.47e-03

Catalytic NodB homology domain of Colletotrichum lindemuthianum chitin deacetylase and similar proteins; This family is represented by the chitin deacetylase (endo-chitin de-N-acetylase, ClCDA, EC 3.5.1.41) from Colletotrichum lindemuthianum (also known as Glomerella lindemuthiana), which is a member of the carbohydrate esterase 4 (CE4) superfamily. ClCDA catalyzes the hydrolysis of N-acetamido groups of N-acetyl-D-glucosamine residues in chitin, converting it to chitosan in fungal cell walls. It consists of a single catalytic domain similar to the deformed (alpha/beta)8 barrel fold adopted by other CE4 esterases, 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. It possesses a highly conserved substrate-binding groove, with subtle alterations that influence substrate specificity and subsite affinity. Unlike its bacterial homologs, ClCDA contains two intramolecular disulfide bonds that may add stability to this secreted protein. The family also includes many uncharacterized deacetylases and hypothetical proteins mainly from eukaryotes, which show high sequence similarity to ClCDA.


Pssm-ID: 200575 [Multi-domain]  Cd Length: 197  Bit Score: 39.18  E-value: 1.47e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1332788139 200 IRQLRAAGMQIGAHTVNHPILATLDAAGMRREIgdskDYLEAVLREPV----RLFAYPNGkpgqDYNADSVAQVKDLG 273
Cdd:cd10951    56 LRRMYNEGHQIASHTWSHPDLTKLSAAQIRDEM----TKLEDALRKILgvkpTYMRPPYG----ECNDEVLAVLGELG 125
CE4_NodB_like_1 cd10960
Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases; This ...
159-282 3.98e-03

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.


Pssm-ID: 200583 [Multi-domain]  Cd Length: 238  Bit Score: 37.98  E-value: 3.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332788139 159 IDALLGVIKYRVPDERVQCVAAI-ETL-------CGGAHDQALMMGDAGIRQLRA---AGMQIGAHTVNHPILATLDAAG 227
Cdd:cd10960     7 FDDLPFVGGLPPGESRQEITEKLlAALkkhgipaYGFVNEGKLENDPDGIELLEAwrdAGHELGNHTYSHPSLNSVTAEA 86
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1332788139 228 MRREIGDSKDYLEAVL-REPVRLFAYPNGKPGQDYNA-DSVAQV-KDLGFLAAVSTVW 282
Cdd:cd10960    87 YIADIEKGEPVLKPLMgKAFWKYFRFPYLAEGDTAEKrDAVRAFlKKHGYRIAPVTID 144
CE4_NodB_like_3 cd10959
Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases; This ...
200-256 8.81e-03

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.


Pssm-ID: 200582 [Multi-domain]  Cd Length: 187  Bit Score: 36.82  E-value: 8.81e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1332788139 200 IRQLRAAGMQIGAHTVNHPILATLDAAGMRREIGDSKDYLEAVLREPVRLFAYPNGK 256
Cdd:cd10959    46 IRRIVDEGHEIGNHGYRHRHPWLRSPWKAIRDLRRAARIIEQLTGRPPRYYRPPWGH 102
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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