1DBG,1OFM,1OFL


Conserved Protein Domain Family
PL-6

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cd14251: PL-6 
Click on image for an interactive view with Cn3D
Polysaccharide Lyase Family 6
Polysaccharide Lyase Family 6 is a family of beta-helical polysaccharide lyases. Members include alginate lyase (EC 4.2.2.3) and chondroitinase B (EC 4.2.2.19). Chondroitinase B is an enzyme that only cleaves the beta-(1,4)-linkage of dermatan sulfate (DS), leading to 4,5-unsaturated dermatan sulfate disaccharides as the product. DS is a highly sulfated, unbranched polysaccharide belonging to a family of glycosaminoglycans (GAGs) composed of alternating hexosamine (gluco- or galactosamine) and uronic acid (D-glucuronic or L-iduronic acid) moieties. DS contains alternating 1,4-beta-D-galactosamine (GalNac) and 1,3-alpha-L-iduronic acid units. The related chondroitin sulfate (CS) contains alternating GalNac and 1,3-beta-D-glucuronic acid units. Alginate lyases (known as either mannuronate (EC 4.2.2.3) or guluronate lyases (EC 4.2.2.11) catalyze the degradation of alginate, a copolymer of alpha-L-guluronate and its C5 epimer beta-D-mannuronate.
Links
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Statistics
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PSSM-Id: 271210
Aligned: 68 rows
Threshold Bit Score: 228.649
Created: 2-Mar-2014
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 15 residues -Click on image for an interactive view with Cn3D
Feature 1:substrate binding site [chemical binding site]
Evidence:
  • Structure:1OFL, Pedobacter heparinus Chondroitinase B with bound Dermatan sulfate hexasaccharide, contacts at 4A

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                         
1DBG_A         28 VASNETLYQVVKEVKPGGLVQIADGTYKDVQLIVSNSGKs----gLPITIKALNPGKVFFTGDAKVELRGEHLILEGIWF 103  Pedobacter he...
1OFL_A          3 VASNETLYQVVKEVKPGGLVQIADGTYKDVQLIVSNSGKs----gLPITIKALNPGKVFFTGDAKVELRGEHLILEGIWF 78   Pedobacter he...
YP_005006469   31 VTSITELQAAINNAAPGDVIILANGVYTATADITISKKGta---aQPITIAAQTIGGAEITGSGGFSIVSPAAYIIIKGF 107  Niastella kor...
YP_003093480   28 VSSLPELQAAIDKSAAGDVILLKNGVYTSTNDIVVRKKGta---aKPITIAAESIGGAEITGAGGIKIAGPSAYIVIRGF 104  Pedobacter he...
ZP_09632353    24 VTSIDELQQAINRAKPGEEIVLKNGVYAAGANITIACTGtk---eKPIIIKAESIGKAEIAGVGGFELIKPATYVIISGF 100  Niabella soli...
YP_006875621   44 VSSLDDLQDAIDAAGPGTRIVLANGTYTVPSAKPLTITGkngtrsAPITIVAASRGGAVLRGERSFVFDASSNVTVSGFS 123  Streptomyces ...
YP_005010635   29 IKTIGHLQKAIDEAKPGDTLLVQSGLYATGNPVTIKQEGtk---eQPIVIMAQTAGQAEITGAGGFAIMSPAKYIVISGF 105  Niastella kor...
ZP_22941685    39 VSSLTELQNAINSAAAGTVITVNNGTYTVPTGKPITITGkrgtkdQPITIVAQSRGGVTLNGEQSFVFDDSVGVTISGFK 118  Amycolatopsis...
YP_003764010   28 VTSLAALQSAMDKANPGDTIVLADGSYSAGSTLSIKRSGts---tAPVTVAAEHTGQATITGSKTFAFASGVSNVVLRGF 104  Amycolatopsis...
ZP_22947443     1 MTSLSALQSAIDKAGPGDEIRLADGSYSAGSAIAIKRSGta---nAPITITAEHVGKAEIKGSTGFSFSSGASHVVLRGF 77   Amycolatopsis...
Feature 1                                                                              # #        
1DBG_A        104 KDGNraiqawkshgpgLVAIYGSYNRITACVFDCFDeansAYITTSltedgkvPQHCRIDHCSFTDKITFDQVINLNNta 183  Pedobacter he...
1OFL_A         79 KDGNraiqawkshgpgLVAIYGSYNRITACVFDCFDeansAYITTSltedgkvPQHCRIDHCSFTDKITFDQVINLNNta 158  Pedobacter he...
YP_005006469  108 KFTHa----------aNHAKMASGTSFCRWTRNTFEt--pGEGEYLql----nGNDHEVDYNTFQNKSNLGRFITVRGvg 171  Niastella kor...
YP_003093480  105 KFTHl----------sGKAETGEGSSFCRWTRNIFEt--tGEGNYLtv----fGSDQQIDHNTFQNKNALGKFIGVRGtg 168  Pedobacter he...
ZP_09632353   101 KFTHa----------aSKARSAPGTSFCRWTHNIFEm--pGKGEYLti----aGNDHEIDYNTFQNKNSMGRILAIRGeg 164  Niabella soli...
YP_006875621  124 FRQStt---------lEIPPTCTYIRLTRNDFQLAD----IEGLHWvm---vrGDEAVIDRNHFHGKTTLGIFLGIEGdg 187  Streptomyces ...
YP_005010635  106 KFTHa----------aSTARTGTGTSFCRWTHNIFEt--eGEGEELti----aGSDHQVDYNTFHNKSTMGRFLAIRGeg 169  Niastella kor...
ZP_22941685   119 FRQS------------TMLDIPPNCSVIRLTRNDFQla-dIEGLHWvl---vrADKTKVDRNHFHHKSTLGVMLRIEGad 182  Amycolatopsis...
YP_003764010  105 KFRGs-----------AKLSVPAGASNNRLTRNDFQl---TADGNWvt---vsGDDTVVDRNVFQNRTSQGVFLQILGps 167  Amycolatopsis...
ZP_22947443    78 KLRHg-----------GSLSVPVGGTHNRLTRLDVQl---TGGGNWvt---lnGDDTEFDHNVLQNRTTQGVFLQVLGpa 140  Amycolatopsis...
Feature 1                                       ####   #  #                      # #  # #         
1DBG_A        184 raikdgsvggPGMYHRVDHCFFSNPQk--pGNAGGGIRIGYYrn--dIGRCLVDSNLFMRQDSEAEIITSKSQENVYYGN 259  Pedobacter he...
1OFL_A        159 raikdgsvggPAMYHRVDHCFFSNPQk--pGNAGGGIRIGYYrn--dIGRCLVDSNLFMRQDSEAEIITSKSQENVYYGN 234  Pedobacter he...
YP_005006469  172 --------sqIAQRLWIHHNYFHKQLpg-gGNGAETLQFGLSgyslsSSYSIIEHNVFEECDGENELISVKASALTIRYN 242  Niastella kor...
YP_003093480  169 --------kqIAERLWIHHNYFHNFSqq-rGNGAEAVQFGLSgfslsSSNSIFEYNLFENCEGENELLSVKSSAITVRYN 239  Pedobacter he...
ZP_09632353   165 --------kqIAERLHIHHNYFYNFPdqggANGAETLQFGLSgfslsTSNSVVEYNLFEKCAGENELISVKASGVVLRYN 236  Niabella soli...
YP_006875621  188 t-------eaMAQGVHIHRNHFSDHTfa-gSNGGEPIRLGVSpralsSAHALVEYNLFERANGDPEAISVKSSDNTIRYN 259  Streptomyces ...
YP_005010635  170 --------sqIAERLWIHHNYFYNFTsqggKNGAEAFQFGLSgfsmsKSNSIVEYNLFEYCEGENELISVKASAVTLRYN 241  Niastella kor...
ZP_22941685   183 d-------dkMASGVEVFRNYFSDHTfg-gSNGGEPIRLGVSpralsTAGAKIENNLFERANGDPEAISVKSSGNFVRYN 254  Amycolatopsis...
YP_003764010  168 --------gaMAKRVHVHHNYFYNHQfs-gSNGGESIRLGLSdhqsyTANALIENNLFEKADGDSEAISVKSSDNVVRYN 238  Amycolatopsis...
ZP_22947443   141 --------kdMAKRVKVHHNYFSNHGft-gSNGGESIRFGLShhqkySAGGVVEYNLFEKADGDSEAISVKSSDNVIRYN 211  Amycolatopsis...
Feature 1                    ##                         #                                         
1DBG_A        260 TYLNCQGTMNFRHGDHQVAINNFYIgndqrfgYGGMFVWGSRHVIACNYFELSEtiksrgnaaLYLNPGamas------- 332  Pedobacter he...
1OFL_A        235 TYLNCQGTMNFRHGDHQVAINNFYIgndqrfgYGGMFVWGSRHVIACNYFELSEtiksrgnaaLYLNPGamas------- 307  Pedobacter he...
YP_005006469  243 TIRNCPAQFTLRHGNRSVVYGNYFSn------TPGLRIFGDDHVIFSNYFENCSta-----ldIGNGDGevayga----- 306  Niastella kor...
YP_003093480  240 TIRDCKAQLTLRHGNFNQVYGNYFNn------TPGIRIFGDDHIIYSNYFENCNsa-----inIGNGGAevadga----- 303  Pedobacter he...
ZP_09632353   237 TIRDCPAQFTLRHGNKCQVYSNYFFn------TPGLRIYGDDHAIFSNYFENCKpa-----itIGNGDGevadga----- 300  Niabella soli...
YP_006875621  260 TIRDSLGGIVLRHGNRTRVDSNYLIg-----gEEGIRIYGNDHVIVNNYLAGLSgr------aMVIGSGterdhlpgesa 328  Streptomyces ...
YP_005010635  242 TIRNCKAQFTLRHGNFCQVYGNYFNn------TPGLRIFGDDHIIYSNYFETCSmg-----inIGNGDGevadgs----- 305  Niastella kor...
ZP_22941685   255 TIRNSLGGIVLRHGNKTLVDSNFILn-----gQEGIRIYGNDHTIVNNYLSGLSsr------aLVVGSGtvrdhfvgesp 323  Amycolatopsis...
YP_003764010  239 TIRDSRGYIVLRHGNRSTVEGNVLF-------GSGIRFHGNDHKIVNNYVANSGgr------aIVFGSGdeadsgp---- 301  Amycolatopsis...
ZP_22947443   212 TIRDSRGFIVLRHGDRSVVEGNILLg------RSGIRFHGNDHKIVNNYVHTTAnr------gIVFGSGneadsgp---- 275  Amycolatopsis...
Feature 1                                                                                         
1DBG_A        333 ----ehaLAFDMLIANNAFINVNGYAIHFNPlderrkeycaanrlkfetPHQLMLKGNLFFKDkpyvypFFKDDyfiagk 408  Pedobacter he...
1OFL_A        308 ----ehaLAFDMLIANNAFINVNGYAIHFNPlderrkeycaanrlkfetPHQLMLKGNLFFKDkpyvypFFKDDyfiagk 383  Pedobacter he...
YP_005006469  307 -pltshdRPDRILIAFNTLVNCSSNFKQGGRtgg-------------lgATFVTVANNIVQGGgaa-asIAGPYtn---- 367  Niastella kor...
YP_003093480  304 -pltshdRPDRVLIVFNTLINNKSNITLNPRspi------------glgATAVTIANNLIQGGdea-avIRGPYvn---- 365  Pedobacter he...
ZP_09632353   301 -qltahdRPDRVLIAFNTLVNNGENIILQARkng-------------mgATAITVADNIVQGGlka-vsLMGDLkd---- 361  Niabella soli...
YP_006875621  329 earrgndAPDRVLIAHNTLLDNTGGTLSGESqrp-------------hePRDVTVADNLLVGQtg--slVEMATtvr--- 390  Streptomyces ...
YP_005010635  306 -altchdRPDRVLIAFNTLISCKSGSIVMGGrdk------------glgATAITVARNIIRGGgpa-asITGPYvn---- 367  Niastella kor...
ZP_22941685   324 esrrgndAADRVLIAHNTLLNNSSTLSGETNrt--------------iePRDCTISDNIFVGSng---dLVAMSttg--n 384  Amycolatopsis...
YP_003764010  302 -tsklhdRPDRDTVAYNTVIGSSSVIDGDGGnf---------------kPKDCVVADNIVEGTsg--tlVTLPSgst--- 360  Amycolatopsis...
ZP_22947443   276 -dsklhdRPDRVVVAYNTVVGTTDAIHGDGGdf---------------kPKDCVLANNILQGTgk---lVSMPGgsd--- 333  Amycolatopsis...
Feature 1                    
1DBG_A        409 nsWTGNVALGV 419  Pedobacter heparinus
1OFL_A        384 nsWTGNVALGV 394  Pedobacter heparinus
YP_005006469  368 pvWTGNMLFNV 378  Niastella koreensis GR20-10
YP_003093480  366 skWEGNVIFNV 376  Pedobacter heparinus DSM 2366
ZP_09632353   362 pvWKNNLFFEV 372  Niabella soli DSM 19437
YP_006875621  391 ftWQGNILFGA 401  Streptomyces venezuelae ATCC 10712
YP_005010635  368 pvWEGNMVFNA 378  Niastella koreensis GR20-10
ZP_22941685   385 ftWSGNILWGS 395  Amycolatopsis decaplanina DSM 44594
YP_003764010  361 vkYEGNITSGG 371  Amycolatopsis mediterranei U32
ZP_22947443   334 vkYEGNIAWGG 344  Amycolatopsis decaplanina DSM 44594

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