Conserved Protein Domain Family
GH20_DspB_LnbB-like

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cd06564: GH20_DspB_LnbB-like 
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Glycosyl hydrolase family 20 (GH20) catalytic domain of dispersin B (DspB), lacto-N-biosidase (LnbB) and related proteins. Dispersin B is a soluble beta-N-acetylglucosamidase found in bacteria that hydrolyzes the beta-1,6-linkages of PGA (poly-beta-(1,6)-N-acetylglucosamine), a major component of the extracellular polysaccharide matrix. Lacto-N-biosidase hydrolyzes lacto-N-biose (LNB) type I oligosaccharides at the nonreducing terminus to produce lacto-N-biose as part of the GNB/LNB (galacto-N-biose/lacto-N-biose I) degradation pathway. The lacto-N-biosidase from Bifidobacterium bifidum has this GH20 domain, a carbohydrate binding module 32, and a bacterial immunoglobulin-like domain 2, as well as a YSIRK signal peptide and a G5 membrane anchor at the N and C termini, respectively. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Statistics
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PSSM-Id: 119334
View PSSM: cd06564
Aligned: 34 rows
Threshold Bit Score: 217.539
Threshold Setting Gi: 123438499
Created: 15-Nov-2005
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
active site
Conserved site includes 10 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:1YHT_A; Aggregatibacter actinomycetemcomitans dispersin B binds glycerol and acetic acid.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                   #                            #                                        
1YHT_A         17 KQTGLMLDIARHFYSPEVIKSFIDTISLSGGNFLHLHFSDh--eNYAIESHLLNQRaenavqgkdg-------------- 80
gi 15673476     1 MEKGLLVDIGRKYWSIAELKRLVLLLQEHKLTHLQLHLNEn--eGFALNFTDSPVSk----------------------- 55
gi 24429540   178 PKRGFSLDIARKHYSADWIKDRIRELGDLKFNELGLHFSDd--qAFRIESDSHPEIvs---------------------- 233
gi 154495917   43 FDRIVHLDMGRKYFTPDWIKSLIDEMAKLGYNQLELDFGNsekgQLRFALEDMSVNytyteqtmvpvdntdaqeepaapv 122
gi 15902101   631 KNKVISIDAGRKYFTLDQLKRIVDKASELGYSDVHLLLGNd---GLRFLLNDMTITangktyasddvkkai--------- 698
gi 29374765   491 LKSVFSIDAGRKYFSVEQLEELVAKASQNGYTDVQLILGNd---GLRFILDDMSVNvngkkynhnrvskai--------- 558
gi 15902101   186 KKKIVSIDAGRKYFSPEQLKEIIDKAKHYGYTDLHLLVGNd---GLRFMLDDMSITangktyasddvkrai--------- 253
gi 121945716   37 LKSVFSIDAGRKFFSADQLKMIIDRAHTDGYTDVQVLLGNd---ALRLLLDDMSVTingktygsdvvkqai--------- 104
gi 160914154   62 LKSVFSIDAGRKYFSTEQLKTIIERAYKNGYTDVQILLGNd---ALRFFLDDMSLEvngkqydsnavkeal--------- 129
gi 123438499   21 TRNAFMLDVARRKMTKDQILQAINSINITCFRYLMLHLSDdqsySLGFITDTLKIGkqti-------------------- 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
1YHT_A            --------------------------------------------------------------------------------
gi 15673476       --------------------------------------------------------------------------------
gi 24429540       --------------------------------------------------------------------------------
gi 154495917  123 etgepveeqpaapvqteepadeeqtaetvmplqeepaapaetvaptapvtdevleqaeesgaangvivynyidvpttktv 202
gi 15902101   699 -----------------------------------------------------------------------------ieg 701
gi 29374765   559 -----------------------------------------------------------------------------qrg 561
gi 15902101   254 -----------------------------------------------------------------------------ekg 256
gi 121945716  105 -----------------------------------------------------------------------------qag 107
gi 160914154  130 -----------------------------------------------------------------------------tkg 132
gi 123438499      --------------------------------------------------------------------------------
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                 #                                       
1YHT_A         81 -iyinpytgkpFLSYRQLDDIKAYAKAKGIELIPELDSPNHMTAIFKLVqkdrgvkylqglksrqvddeIDITNADSITF 159
gi 15673476    56 -----------KYSENMLKELKEFAKTHEITLIPDFDSPGHMGSLLEQNpefalp--------dsnqqaVDVTNPAVIDW 116
gi 24429540   234 ---------deHLTKAEMKEIIDLAASRHITVVPEIDSPGHLGAVIAAHpdlqlrna----qgtatrgaIDISKPEAAKI 300
gi 154495917  203 ylnaalpadgeYITESEMKGIIAHAKDKGIEIVPLLNSPGHFGAVLDGVrdengapvn---fsynnsnsLDITNEEAVAF 279
gi 15902101   702 tkayyddpngtALTQAEVTELIEYAKSKDIGLIPAINSPGHMDAMLVAMeklgiknpqa-hfdkvskttMDLKNEEAMNF 780
gi 29374765   562 nnayyndpngnALTQKEMDRLLAFAKARNINIIPVINSPGHMDALLVAMeklaiknp----afdgskrtVDLGNQKAVNF 637
gi 15902101   257 tndyyndpngnHLTESQMTDLINYAKDKGIGLIPTVNSPGHMDAILNAMkelgiqnpnfsyfgkksartVDLDNEQAVAF 336
gi 121945716  108 nkayyddpngnALTQTDMDAVLKYAAARDINIIPVINSPGHMDAILTAMaqlgiknp----afngskrtVDLNNDTAIAF 183
gi 160914154  133 nqsyyndpngnALTQAEMDEILAYAAERGMNIIPVINSPGHMDSILVAMetlgiqnp----qfdgsvrtVDLDNEEAVAF 208
gi 123438499   81 --------gngWLTDSDLAEIVSLAKSKSLYLIPDIDAPSHVGSWYKSYqssgestd-----ifsdsntLDIEKLDSSSG 147
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                 ##                                                      
1YHT_A        160 MQSLMSEVIDIFgd-tsQHFHIGGDEFgys-----------------------vesNHEFITYANKLSYFLEKkGLKTRM 215
gi 15673476   117 IMGIIDKIVDIFpd--sDTFHIGADEFidfrqiekypylv---ektrekygnkasgLEFYYDYVNQLTEHLQKkGKQVRI 191
gi 24429540   301 VDDLLNEYADLFp---gSQFHLGADEYqalvvpnpeasyptlaaaarkaygsggtvADLTTGWLNGRAKTVMAhDRTPRA 377
gi 154495917  280 GQAVVLKYAEWFkgqgcDTFNIGADEFandiypsggm---------gfghlvwtqqYHHFVDYVNTLADKLQEmGYTVRA 350
gi 15902101   781 VKALIGKYMDFFag-ktKIFNFGTDEYandatsaqg-----------wyylkwyqlYGKFAEYANTLAAMAKErGLQPMA 848
gi 29374765   638 TKAIISKYVAYFsa-hsEIFNFGGDEYandvdtggw------------aklqssgrYKDFVAYANDLAKIIKDaGMQPMS 704
gi 15902101   337 TKALIDKYAAYFak-ktEIFNIGLDEYandatdakgwsvlq-adkyypnegypvkgYEKFIAYANDLARIVKShGLKPMA 414
gi 121945716  184 TKALLQKYVMYFkg-haTIFNFGSDEYandvdtggw------------aklqqsgtYKKFVAYVNDLAAMAKNaSLKPMV 250
gi 160914154  209 TKALVKKYAEYFgsksvEIFNLGCDEYandkntggw------------anlqksglYKKFVAYVNDLSAIVKAaGMKPMC 276
gi 123438499  148 VYEIYKKCMTIFkd-vsNYINIGVDEVpgn-----------------------tyyANQLASHINKINQIAKEnNYKTVV 203
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1         #                       #                                        #              
1YHT_A        216 WNDGLIknt---feqINPNIEITYWSydgdtqdkneaaerrdmrvsLPELLAKGFTVLNYNSYYLYIVpkasptfsqdaa 292
gi 15673476   192 WNDGFLrkdlqslvpLNKNVEVCYWTnwdk------------gmaeVKEWLTKGYTLINFCDNDLYYVlgee----agys 255
gi 24429540   378 WNDGFFkdt---svePLKDIKVAYWTgkei------------garpPAEYLGEGRQVLNYNDEFLYYVlgqpq---tfvy 439
gi 154495917  351 FNDGINygg---qtgVENDIQVCYWTsgwpg----------ynvasASALAAQGFTMINTHGDYYYVLgkns-----amt 412
gi 15902101   849 FNDGFYyedk-ddvqFDKDVLISYWSkgwwg----------ynlasPQYLASKGYKFLNTNGDWYYVIgnhk----qdea 913
gi 29374765   705 FNDGIYynsddsfgtFDPEIIISYWTagwsg----------ydvakPEYFVQKGHKIFNTNDAWYWVAgnvd-----sgi 769
gi 15902101   415 FNDGIYynsdtsfgsFDKDIIVSMWTggwgg----------ydvasSKLLAEKGHQILNTNDAWCYVLgrna----dgqg 480
gi 121945716  251 FNDGIYydnntsfgtFDKDLIVSYWTagwgg----------ydvakPEFLTDKGLKIMNTNDGWYWVLgrvd-----gdl 315
gi 160914154  277 FNDGIYynskeefgtFDKDLIISYWTsgwwg----------ydvakPSFFAERGHKILNTNDGWYWVIgnydk--sehgn 344
gi 123438499  204 WNDALNgkl---lqqLDSDITIMYWHdsd--------------vntFEALLNTKNPIKNAYYDTNYDNvhdl----depe 262
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
Feature 1                                              # #                            
1YHT_A        293 FAAKDVIKNwdlgvwdgrntknrvqntheIAGAALSIWGEdakalkdETIQKNTKSLLEAVIHKTNGD 360
gi 15673476   256 YPTAEKLERegkiqkfsgqqylnqeemkaVRGTYFSIWADnaaaksvSEILDDLSKVLPVFMKIYGGN 323
gi 24429540   440 PTGERIYEQwtprvlrgtt-avdakyddqILGGSFAVWGDfpnaqtqAQVAEGIRLPLAATVQKLWDP 506
gi 154495917  413 EGKIDAADFdaasfid-------gsviaePAGAMFCIWSDypdaqtqDEVMNGALPYMTGFASALGGG 473
gi 15902101   914 YPLSKAVENsgkvpfnqlastkypevdlpTVGSMLSIWADrp---saEYKEEEIFELMTAFADHNKDY 978
gi 29374765   770 YQYDDALANmskkaftdv---pagspnlpIIGSIQCVWYDdp---rrDYDFERIYTLMDTFSENYREY 831
gi 15902101   481 WYNLDQGLNgikntpitsv-pktegadipIIGGMVAAWADtp---saRYSPSHLFKLMRHFANANAEY 544
gi 121945716  316 YSYKTALASlaskkftdv---pgassavpIIGSVQAVWADdp---saQLDMPALLKLMDQFSTAYAPY 377
gi 160914154  345 GYTYDSAVNgikgkdftsvtgakpednldLIGSMQAVWCDyp---eeVYEEDVVLGLMDLFSETHSEY 409
gi 123438499  263 YQKGKITKFvn----------------nlINNNILCLWGEdse-ditHDQIINFINDVQNEMIKNNKI 313

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