Conserved Protein Domain Family
RhgB_N

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pfam09284: RhgB_N 
Rhamnogalacturonan lyase B, N-terminal
Members of this family are found in both fungi, bacteria and wood-eating arthropods. The domain is found at the N-terminus of rhamnogalacturonase B, a member of the polysaccharide lyase family 4. The domain adopts a structure consisting of a beta super-sandwich, with eighteen strands in two beta-sheets. The three domains of the whole protein rhamnogalacturonan lyase (RGL4), are involved in the degradation of rhamnogalacturonan-I, RG-I, an important pectic plant cell-wall polysaccharide. The active-site residues are a lysine at position 169 in UniProtKB:Q00019 and a histidine at 229, Lys169 is likely to be a proton abstractor, His229 a proton donor in the mechanism. The substrate is a disaccharide, and RGL4, in contrast to other rhamnogalacturonan hydrolases, cleaves the alpha-1,4 linkages of RG-I between Rha and GalUA through a beta-elimination resulting in a double bond in the nonreducing GalUA residue, and is thus classified as a polysaccharide lyase (PL).
Statistics
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PSSM-Id: 401282
View PSSM: pfam09284
Aligned: 54 rows
Threshold Bit Score: 317.591
Threshold Setting Gi: 524453130
Created: 21-May-2020
Updated: 7-Aug-2020
Structure
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Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
XP_007280130  25 FGVTTSGSNLVVDAGSsnSLVFSVSKSSCDINSIKY----RGNELQYG-SKGSHISSGLGTATVESTTIKAstgNVIKIT 99  Colletotrichum ...
XP_002836824  21 WGYTDDGSNYVIDVGS--KLVFKVSKTNGDINSIVY----RGTEYQGYsGKNSHIQSGLGRSTVTIASHTSp-aNLLMVT 93  Tuber melanospo...
EKD21520      22 WGYTDNGSAYVIDTGT--ALVFAVSKSNGDITSMKY----NGVEYNGYgGKNSHVQSGLGASTVTIQQYTTp-aNIIKVT 94  Marssonina brun...
ELA27422      21 wGWTDNGSEYVIDSGS--DLVIKVTKCCGDISSLNY----KGVEYNGWgGKNSHVESGLGTSTVSITTYSN----VIKVS 90  Colletotrichum ...
XP_003041718  21 wGWNDQNGNYVIDSGA--DLVISVSKSNGDINSLKY----KGQEFNGWgGKNTHVESGLGASTVSIASVGS---NVIKVS 91  [Nectria] haema...
EMR67284      21 WGYTDDGSNYVIDSGS--KLVIKVSKSTGDMTSIKLcnldNGVEYNGYdGKNSHVESGLGASTVAIQQFTDp--HVIKVS 96  Eutypa lata UCREL1
CBY01450      21 wGHTDDGSNYVIDTNA--NLVVKVSKENGDMTSIVY----RGVEYNGQnGKNSQVENGLPGATVSIKNEGS---NVIKVT 91  Leptosphaeria m...
XP_008024796  21 WGYTDDGRNYVIDTNA--NLIVKVSKTNGDMTSINY----RGVEYNGQnGKNSHVESGLGAGTVTIKQYTSp-aNIIKVT 93  Exserohilum tur...
CDB99105      39 FGYTEDSTNYTIDTGA--NLVFKVKRSNGDISSLIY----NGTDYNGYtNKNSHVETGLGQSDVTISQPSS---SVIMVK 109 Firmicutes bact...
Q82LA3        40 FGYTDDGSNYVVDTGA--NLVFKVSKTNGDLTSLVY----RGTEYQGYgGKNSHVESGLGTSAVTIAQSGS----TILVS 109 Streptomyces av...
XP_007280130 100 CTTSTLTHYLIVKEGEANIYMATYiTAEPDIGELRFIARLNKDILPSe--YP--FGAVSTTAGSSSTVEGSDVFVV--SG 173 Colletotrichum ...
XP_002836824  94 ITYGTLVHYIVARSGQNDIYLLTN-KGDASVAALRFILRLKPNIFPH----D--LSTPDFYDNVGATVEASDVVRNs-NG 165 Tuber melanospo...
EKD21520      95 VVYGTLIQTYIARYGNANIYMLTN-KGDASVPALRYIVRIPPGRLPR----P--LTDSDYYDPGS-TIEASDISLSsaNG 166 Marssonina brun...
ELA27422      91 VVHGTLKHWIFVRYGNNNVYLFTN-KADDSVSAMRYIVRIKGGIFSH----A--STESDFYDADSTIIEAQDINVNs-AG 162 Colletotrichum ...
XP_003041718  92 VQHGTLKHYIVVRYKNNNVYLFTN-KADTSISAMRYIVRIKPGIFSHastDAemLTSIDYYDPGSSYIEASDVSINs-NG 169 [Nectria] haema...
EMR67284      97 VTHGTLKHYLFVRYGNNNVYIFTN-KADDSVTVQRYIVRIPGGIFGS---DP--DADTDWIPSGASTVEASDVNEDdgTG 170 Eutypa lata UCREL1
CBY01450      92 AELGTLTHSLVFRNGNPNVYIFIN-KVDLSIPASRYTVRIPPGIFKR-------DGQADWAPEIAVAGEWGDIESY--SG 161 Leptosphaeria m...
XP_008024796  94 VNVGTLVHTLVFRYGNANVYIFMN-KKDTSITVSRYIVRIPGNIFTN---NP--NEDTDWVPDGAGAIESGDINGI--NG 165 Exserohilum tur...
CDB99105     110 VVYGTLEQYYVARKGENNIYMFTY-IADDSVTVTRYIVRLKPSLFPV----L--NTSNSWYSSYS-TLEAKDIFTDtsTG 181 Firmicutes bact...
Q82LA3       110 VTYGTLKHYYAARSGENNVYVWTN-KADTSVSATRYIVRVKAGLFLN--------DEPDSYTYAPTTVEAADVFAKa-DG 179 Streptomyces av...
XP_007280130 174 QTRSKFYSSE---RFIDDKVRCVYGTspeEIHVCISVnpsTGFELSSGGPFFRDINTNNAGD---STNLYNYMNSGHVQT 247 Colletotrichum ...
XP_002836824 166 YTKSKHYQGSnygRVMDFDYVGKTTG---KVGVWLIR---SNHEKASGGPNVAE------DL----YEILFY-SMCHTDP 228 Tuber melanospo...
EKD21520     167 YTKSKHYQGSnygRTIDYDYVGKSTS---SVGVWLIR---SNREKASGGPFFRSLTRGCSPDaedLYEILYY-NMGTTDP 239 Marssonina brun...
ELA27422     163 LTKSKHYQGSnygRTIDYDYVGRTKS---DVGLFMIR---SNHEKASGGPFFRSLVRRADPTgedLYDIYYY-NMGHTDP 235 Colletotrichum ...
XP_003041718 170 ITKSKHYQGNtygRTMDYDYVGKSNG---KVGLYMIR---SNHEKASGGPFFRSLLTRADATgedLYDIYYY-NMGSTDP 242 [Nectria] haema...
EMR67284     171 HTYSKHYSGLqygRVMDFDYVGYTTD---SVGLYMIR---SNHEKASGGPFFRSLQRRGGSGgidLYDIYYY-NMGHTDV 243 Eutypa lata UCREL1
CBY01450     162 LTWSKHYTGRnygRTMDYDYIGYQNA---NVGMYLIR---SNREKSSGGPFFRSMLRRGGPDg---NDLYEIFSTTQGHT 232 Leptosphaeria m...
XP_008024796 166 QTWSKHYSGKlygRTMDYDWVGYTNR---NVGMYLIR---SNHEKASGGPFFRSLVRRGGSGgpdLYDIYHY-NMGHTDV 238 Exserohilum tur...
CDB99105     182 YTYSKHYSDT---RVMDYNYTGISNG---NVGAYIVR---SNHEKASGGPFYRSLIRDNTDVavnLYEILYY---GMAQI 249 Firmicutes bact...
Q82LA3       180 QTRSKHYSKL---RVVDYDYIGWSTG---AVGLWMVR---SNHEKASGGPFYRSLLRHQSADgggLYEILYY---GENQT 247 Streptomyces av...
XP_007280130 248 EAFRMGLHGPYVMSFSRSGIPKATD-----FNYDFYADLSLKG 285 Colletotrichum gloeosporioides Nara gc5
XP_002836824 229 E--RWGLHGPYVLSFTDGDTPKKELfa-rnPNWSWFDTLGIKG 268 Tuber melanosporum Mel28
EKD21520     240 E--RWGLQGPYVLSFTNGATPNTALfa-rkADWSWMDTLGIKG 279 Marssonina brunnea f. sp. 'multigermtubi' MB_m1
ELA27422     236 M--RTGLQGPSVISFTNGEAPNSNLfa-rkADWSWFDDLGLDG 275 Colletotrichum fructicola Nara gc5
XP_003041718 243 M--RFGLQGPSVLTFTDGGAPNSNLfa-rnADWTWIDGLGLDG 282 [Nectria] haematococca mpVI 77-13-4
EMR67284     244 M--RLGLQGPSVLSFTDGGAPNNALfa-hkADWSWFDSLGIDG 283 Eutypa lata UCREL1
CBY01450     233 EILRLGLHGPSVLAFTDNGAPPNKYlfarnAELGWVDSINIKG 275 Leptosphaeria maculans JN3
XP_008024796 239 M--RFGLQGPSVLHFTDNGAAPNSNlfarnANWDWFDALEIDG 279 Exserohilum turcica Et28A
CDB99105     250 DVKRYGLQGPYVLAFTDGGEPSSKLya-gnLKTDWIDSLGIHG 291 Firmicutes bacterium CAG:41
Q82LA3       248 EAQRFGLQGPYVIAFTDGGAPSSSLyp-gnLTTSWADSLGIFG 289 Streptomyces avermitilis
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