NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|124259029|gb|ABM94023|]
View 

hypothetical protein Mpe_A1062 [Methylibium petroleiphilum PM1]

Protein Classification

polysaccharide deacetylase family protein( domain architecture ID 10181053)

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 Caulobacter vibrioides oligosaccharide deacetylase HfsH

CATH:  3.20.20.370
CAZY:  CE4
EC:  3.-.-.-
Gene Ontology:  GO:0016810|GO:0005975
PubMed:  12644381
SCOP:  3001025

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CE4_GLA_like_6s cd10967
Putative catalytic NodB homology domain of gellan lyase and similar proteins; This family is ...
 40-237 1.85e-37

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: 130.96  E-value: 1.85e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029  40 ALTITCDDSARRDQDIVSVLDSQNLKGVISVSPDLVGTDGFLDYAALRDMQAGGHELAFHGNDHSPFTDIhPLRKLTDSV 119
Cdd:cd10967    2 AVSLTFDDGYAQDLRAAPLLAKYGLKGTFFVNSGLLGRRGYLDLEELRELAAAGHEIGSHTVTHPDLTSL-PPAELRREI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029 120 AEGLSRLQDQ-GLSTQTVVYPCGNNNRRIRQALAPFFRAGVSTWFGVNSGKRINRYSIR-RVPFGAYASQHAPSEHWYRD 197
Cdd:cd10967   81 AESRAALEEIgGFPVTSFAYPFGSTNPSIVPLLARGFIAARGVGGGGNPPNPSDPPADPaDCHNADSLALGGPELLLAPD 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 124259029 198 MIDVALREPRWIILMLHPGSTEHTP--DHTAMLQRLTQYALE 237
Cdd:cd10967  161 LLDAAKKNGGWLVLWGHSVEGDGTKysVSWEALEALLAYLAE 202
 
Name Accession Description Interval E-value
CE4_GLA_like_6s cd10967
Putative catalytic NodB homology domain of gellan lyase and similar proteins; This family is ...
 40-237 1.85e-37

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: 130.96  E-value: 1.85e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029  40 ALTITCDDSARRDQDIVSVLDSQNLKGVISVSPDLVGTDGFLDYAALRDMQAGGHELAFHGNDHSPFTDIhPLRKLTDSV 119
Cdd:cd10967    2 AVSLTFDDGYAQDLRAAPLLAKYGLKGTFFVNSGLLGRRGYLDLEELRELAAAGHEIGSHTVTHPDLTSL-PPAELRREI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029 120 AEGLSRLQDQ-GLSTQTVVYPCGNNNRRIRQALAPFFRAGVSTWFGVNSGKRINRYSIR-RVPFGAYASQHAPSEHWYRD 197
Cdd:cd10967   81 AESRAALEEIgGFPVTSFAYPFGSTNPSIVPLLARGFIAARGVGGGGNPPNPSDPPADPaDCHNADSLALGGPELLLAPD 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 124259029 198 MIDVALREPRWIILMLHPGSTEHTP--DHTAMLQRLTQYALE 237
Cdd:cd10967  161 LLDAAKKNGGWLVLWGHSVEGDGTKysVSWEALEALLAYLAE 202
CDA1 COG0726
Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ...
 40-152 1.54e-07

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: 50.43  E-value: 1.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029  40 ALTITCDDSARRD-QDIVSVLDSQNLKGVISVSPDLVGTDGfldyAALRDMQAGGHELAFHGNDHSPFTDIhPLRKLTDS 118
Cdd:COG0726   21 AVALTFDDGPREGtPRLLDLLKKYGVKATFFVVGSAVERHP----ELVREIAAAGHEIGNHTYTHPDLTKL-SEEEERAE 95

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 124259029 119 VAEGLSRLQDQ-GLSTQTVVYPCGNNNRRIRQALA 152
Cdd:COG0726   96 IARAKEALEELtGKRPRGFRPPYGRYSPETLDLLA 130
 
Name Accession Description Interval E-value
CE4_GLA_like_6s cd10967
Putative catalytic NodB homology domain of gellan lyase and similar proteins; This family is ...
 40-237 1.85e-37

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: 130.96  E-value: 1.85e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029  40 ALTITCDDSARRDQDIVSVLDSQNLKGVISVSPDLVGTDGFLDYAALRDMQAGGHELAFHGNDHSPFTDIhPLRKLTDSV 119
Cdd:cd10967    2 AVSLTFDDGYAQDLRAAPLLAKYGLKGTFFVNSGLLGRRGYLDLEELRELAAAGHEIGSHTVTHPDLTSL-PPAELRREI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029 120 AEGLSRLQDQ-GLSTQTVVYPCGNNNRRIRQALAPFFRAGVSTWFGVNSGKRINRYSIR-RVPFGAYASQHAPSEHWYRD 197
Cdd:cd10967   81 AESRAALEEIgGFPVTSFAYPFGSTNPSIVPLLARGFIAARGVGGGGNPPNPSDPPADPaDCHNADSLALGGPELLLAPD 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 124259029 198 MIDVALREPRWIILMLHPGSTEHTP--DHTAMLQRLTQYALE 237
Cdd:cd10967  161 LLDAAKKNGGWLVLWGHSVEGDGTKysVSWEALEALLAYLAE 202
CE4_DAC_u1_6s cd10970
Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide ...
 40-215 5.18e-17

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: 76.97  E-value: 5.18e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029  40 ALTITCDDSARRDQDIV-SVLDSQNLKGVISVSPDLVGTDGFLDYAALRDMQAGGHELAFHGNDHSPFTDIHP--LRK-L 115
Cdd:cd10970    2 KVSLTFDDGYESQYTTAfPILQEYGIPATAAVIPDSIGSSGRLTLDQLRELQDAGWEIASHTLTHTDLTELSAdeQRAeL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029 116 TDSVAEGLSRLQDQGLStqTVVYPCGNNNRRIRQALAPFFRAGVSTWFGVNSGKRINRYSIRRVPFGAYASQHApsehwY 195
Cdd:cd10970   82 TESKRWLEDNGFGDGAD--HFAYPYGRYDDEVLELVREYYDLGRSGGGGPNGRPPLDPYRLRRVTGEADTTTEE-----V 154

                        170       180
                 ....*....|....*....|
gi 124259029 196 RDMIDVALREPRWIILMLHP 215
Cdd:cd10970  155 KTLLDRAAAYNQWLILMFHD 174
CE4_NodB_like_5s_6s cd10918
Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a ...
 43-180 1.75e-12

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: 63.77  E-value: 1.75e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029  43 ITCDDsARRDQ--DIVSVLDSQNLKGVISVSPDLVGT-----------DGFLDYAALRDMQAGGHELAFHGNDHSPFTDI 109
Cdd:cd10918    4 LTFDD-GYRDNytYALPILKKYGLPATFFVITGYIGGgnpwwapapprPPYLTWDQLRELAASGVEIGSHTHTHPDLTTL 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124259029 110 hPLRKLTDSVAEGLSRLQDQ-GLSTQTVVYPCGNNNRRIRQALAP-FFRAGVSTWFGVNSgKRINRYSIRRVP 180
Cdd:cd10918   83 -SDEELRRELAESKERLEEElGKPVRSFAYPYGRYNPRVIAALKEaGYKAAFTTDPGLNS-PGDDPYALPRIN 153
CDA1 COG0726
Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and ...
 40-152 1.54e-07

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: 50.43  E-value: 1.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029  40 ALTITCDDSARRD-QDIVSVLDSQNLKGVISVSPDLVGTDGfldyAALRDMQAGGHELAFHGNDHSPFTDIhPLRKLTDS 118
Cdd:COG0726   21 AVALTFDDGPREGtPRLLDLLKKYGVKATFFVVGSAVERHP----ELVREIAAAGHEIGNHTYTHPDLTKL-SEEEERAE 95

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 124259029 119 VAEGLSRLQDQ-GLSTQTVVYPCGNNNRRIRQALA 152
Cdd:COG0726   96 IARAKEALEELtGKRPRGFRPPYGRYSPETLDLLA 130
CE4_DAC_u4_5s cd10973
Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide ...
 80-181 9.74e-06

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: 44.57  E-value: 9.74e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029  80 FLDYAALRDMQAGGHELAFHGNDHSPFTDIHP------LRKLTDSVAEGLSRLQDQ-GLSTQTVVYPCGNNNRRIRQALA 152
Cdd:cd10973   45 YLSWDQIREMAKYGVEIANHSYSHPHLVRLGEkmqeqwLEWIRQDIEKSQQRFEKElGKKPKLFAYPYGEYNPAIIKLVK 124

                         90       100       110
                 ....*....|....*....|....*....|..
gi 124259029 153 pffRAGVSTWFGVNSGKRI---NRYSIRRVPF 181
Cdd:cd10973  125 ---EAGFEAAFQQSGGVVSagtDLTALPRFPL 153
CE4_u11 cd10942
Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase ...
 85-215 1.88e-05

Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily; This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily.


Pssm-ID: 200567 [Multi-domain]  Cd Length: 252  Bit Score: 44.78  E-value: 1.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029  85 ALRDMQAGGHELAFHGNDHSPFTDIHPLRKlTDSVAEGLSRLQDQGLSTQTVVYPCGNNNRRIRQALA------------ 152
Cdd:cd10942   65 ELEAILAHGHEIGLHGWQHEPWAGLSPLEE-DDLINRSLSIAERLGLAPVGFRPPGGALGAHTLALLAkhgiryvslagt 143

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124259029 153 ----PFFRAGVST----WFGVNSGKRINRYSIRRVPFGAYASQHAPSEHWYRDMIDVALREPRWIILMLHP 215
Cdd:cd10942  144 grslATMPDGLAVlpfaWAAVDGFYYLDSFDGLRGPPQEEVDTPAALAQALRSALDAVVARGGFLTIVFHP 214
CE4_SF cd10585
Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate ...
 46-144 8.04e-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: 38.97  E-value: 8.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124259029  46 DDSARRD-----QDIVSVLDSQNLKGVISVSPDLVGTDGFLDYAA----LRDMQAGGHELAFHGNDHSPFTDIH-PLRKL 115
Cdd:cd10585    8 DDPAFEGspaalQRLLDLLEGYGIPATLFVIPGNANPDKLMKSPLnwdlLRELLAYGHEIGLHGYTHPDLAYGNlSPEEV 87

                         90       100       110
                 ....*....|....*....|....*....|
gi 124259029 116 TDSVAEGLSRLQDQ-GLSTQTVVYPCGNNN 144
Cdd:cd10585   88 LEDLLRARRILEEAgGQPPKGFRAPGGNLS 117
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH