3NJX,3NJV


Conserved Protein Domain Family
RGL4_N

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cd10320: RGL4_N 
Click on image for an interactive view with Cn3D
N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase
The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold; the middle and C-terminal domains are both putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.
Statistics
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PSSM-Id: 199907
Aligned: 37 rows
Threshold Bit Score: 140.987
Created: 8-Jun-2011
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
active sitecatalytic site
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:3NJV: Aspergillus aculeatus rhamnogalacturonan lyase binds rhamnogalacturonan-derived substrate, contacts at 4 A
  • Comment:The N-terminal domain contributes the catalytic and the majority of substrate binding residues, the C-terminal domain contributes a few substrate binding residues.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                        
3NJX_A         2 FGITTSSs------------------aYVIDTnap----nqLKFTVsr----------------------------sSCD 31  Aspergillus acu...
3NJV_A         2 FGITTSSs------------------aYVIDTnap----nqLKFTVsr----------------------------sSCD 31  Aspergillus acu...
Q2U5P7        39 FSIALAKsn-----------------gHIVDVqldgqdllgPVDGNagk--------------------------gpYLD 75  Aspergillus ory...
XP_774896     11 ALLAVTGvagkity-------setndtITLSSd-------rLTLGVnktlgamtglefdn---vdvlgpvsgrigmgYFD 73  Cryptococcus ne...
Q5AZ85         7 FSLAAAAsvaraalt-----atendtsIVLENdr-----lrATFDKgrgsiidlyldgqd----flgpqsgstgigpYLD 72  Emericella nidu...
CBY00247      21 IKSSEDSs------------------aINISNd-------rLSFSVlkssgavnklsl-------drqnllgtgrgpYLD 68  blackleg of rap...
CBX93397      74 RSLTATAalllssttlavlnvsqnnnsLTLSNe-------rLVASVtktrgsinlltldgq--nllgtesgntgigpYLD 144 blackleg of rap...
ADU33331      18 LSPVDAAv------------------tLTVDGl-------aATIRNdyvelnfkadatistvnvqgtnlaasgvksfYLD 72  mountain pine b...
ADU33329      15 ISVSLAK--------------------VTLTTng-----laATVSNgnvevvfkadatvsavkvngvnivstsqktfYLD 69  mountain pine b...
YP_004455650   1 MKLEVQGl------------------nCFLENkq-----lqVSFSQngtvhslkyqgkellgnldgakndpnkkssfYCD 57  Melissococcus p...
Feature 1                              #                                                         
3NJX_A        32 ITSIIHYgtel-------qysSQGSHIGsglg-satVTATQsg-------------dYIKVTCVT------DTLTQYMVV 84  Aspergillus acu...
3NJV_A        32 ITSIIHYgtel-------qysSQGSHIGsglg-satVTATQsg-------------dYIKVTCVT------DTLTQYMVV 84  Aspergillus acu...
Q2U5P7        76 CSCIPSGfw----------tpGSGAHLElin--gtdSTGTA----------------YGGLYMSAtyagtnQTLSQWFFL 127 Aspergillus ory...
XP_774896     74 CYCIPAVntsvwtpdnpnpqsSRHYYVGqsq--masFEVHQgndr--------nnnpWIGLIMSEt----yEGTGQFFQQ 139 Cryptococcus ne...
Q5AZ85        73 CYCTPSGfyt---------agSTNPVTElvq--gtdSTGTKyagiilndtytptgqeFQQYWFLRd----gETGFHMFSR 137 Emericella nidu...
CBY00247      69 CHCTEAGqwvp------grgaTYKLVTGndsa-gkaYAGAImsqeyq-----gtgkvLEQYWFLRd----gETGLHVFAR 132 blackleg of rap...
CBX93397     145 CYCTPSGfw----------tpGRGRDVTyklyngtdSTGTRyggismgetyaptgqrLEQYWFLRe----gETGLHTFSR 210 blackleg of rap...
ADU33331      73 WNDNGEGvf----------npSSIHIVEqt-----sSRVHFy---------------WLQENIENv----fTIELHYVME 118 mountain pine b...
ADU33329      70 WNENGQVtf----------npSELKVGEns-----dSLAHFy---------------WIQNGASNq----fHIEFHYVMV 115 mountain pine b...
YP_004455650  58 YHDGKPRnl----------qpTQLKIIEns-----dHCLHIa---------------YLDLTSPL------NLEYHIFLL 101 Melissococcus p...
Feature 1                                      # # # # #                            #            
3NJX_A        85 hng----dpIIHMATYita--------epsIGELRFIARLns--dLLPNEepfgdv-sttadGTAIEG------------ 137 Aspergillus acu...
3NJV_A        85 hng----dpIIHMATYita--------epsIGELRFIARLns--dLLPNEepfgdv-sttadGTAIEG------------ 137 Aspergillus acu...
Q2U5P7       128 rge----etGLHAFSRvtyfnet-tpslrsLGELRTLFRPst--dLWTHFs-----------TSDGNYgpkplgs--nsg 187 Aspergillus ory...
XP_774896    140 wwflrdgepGYHTFTRlqfdngtegidlgnLQEFRQVISPns--dIWTHLv-----------TNDVQYghlpsdeatgnq 206 Cryptococcus ne...
Q5AZ85       138 l--------AYYNETTpfl---------rnLQELRTLFRPnt--dLWTHLtssdlqtaplpsDEAIAEqiv--------- 189 Emericella nidu...
CBY00247     133 ---------AKYSNAQtps--------ggdLGEFRQLFRPsa--sVWTHLsssdem-yaplpDTSGAPvv---------- 182 blackleg of rap...
CBX93397     211 ---------VVYKNETspf--------lrnLQEFRTLFRPnhnppLFTHFvtnekf-saprpDTTGQVtv---------- 262 blackleg of rap...
ADU33331     119 ed-----isGIYSYAKytndk----syavtLGETRMVYRFqa--sILTQGtnqvrs-gttptTVDLNQctt--------- 177 mountain pine b...
ADU33329     116 dg-----vsGIYSWAKyinsq----sgtvsLGETRTIYRFds--sILTQGtnqars-gtlylYSYLNTqtk--------- 174 mountain pine b...
YP_004455650 102 nd-----eaCIYGYIVaktte-----qemtIGELRTVYRLnh--sLFPIAytserq-giqpkASYLAKfkq--------- 159 Melissococcus p...
Feature 1             #                     ##                                                   
3NJX_A       138 ----SDVFLVGs-----------eTRSKFYSSeRFIDDQRHCIAGd--------aHRVCMILNQyesssGGPFHRDINSN 194 Aspergillus acu...
3NJV_A       138 ----SDVFLVGs-----------eTRSAFYSSeRFIDDQRHCIAGd--------aHRVCMILNQyesssGGPFHRDINSN 194 Aspergillus acu...
Q2U5P7       188 lvvqDATTYIGnvtddpyvsqysdYFTKYTLAeSWRNHDVHGLFSdgssssdgstFGAWLVHNTvetyyGGPLHSDLVVD 267 Aspergillus ory...
XP_774896    207 ttvqDATWYYNitegnpyrtessdYFTKYEWAdLYGDHFAHGFYAdgtas-ngstLGFWTVFNNlegytGGPLRSDLVVD 285 Cryptococcus ne...
Q5AZ85       190 --vqDATWRLNntpddayyqqfseYFTKYTFSnHWRDNDVHGLYAdgsts-dgttYGAWLVMNTkdtyyGGPLHSDLTVD 266 Emericella nidu...
CBY00247     183 ---qDATTDLSskkddpyvkqmsdYFTKYMFSeDWRDQTVHGMYAdgskvadgstFGAWLVMNTkdtyfNGPTHSDLTVD 259 blackleg of rap...
CBX93397     263 ---qDATWWLPnkespy-vkgvgdYFTKYTFQdTWRDHKAHGMYAdgsgsgngstYGAWLVHNTvdtyyNGPVHSDLVVD 338 blackleg of rap...
ADU33331     178 --vqDSTWQFPng----------tYYSKYDYAaYIRQINYQGVYGn--------gFGAFVVSPSreyhgGGPLKQDLTVH 237 mountain pine b...
ADU33329     175 --vqDETWQLAdg----------tYYTKYDYAgYLRETSYQGVYGn--------gYGAFVISPSreyhaGGPLKQDLLIH 234 mountain pine b...
YP_004455650 160 --lqDETFELPdgsky----tnssVYSKYDYAgYFKDNNFWGQYGd--------qFGCWFIPIDqsyfpSGPLKQDLLVH 225 Melissococcus p...
Feature 1                # #    #                                         
3NJX_A       195 NggsynALYWYMNSGAVq------tESYRmGLHGPYSMYFSr--------SGTPSTS 237 Aspergillus aculeatus
3NJV_A       195 NggsynALYWYMNSGHVq------tESYRmGLHGPYSMYFSr--------SGTPSTS 237 Aspergillus aculeatus
Q2U5P7       268 G-----IVYNYLVSGHHgaptpnltHGFD-RTWGPQFYYFNr--------GDSETTL 310 Aspergillus oryzae RIB40
XP_774896    286 T-----NIYNYYASNHRgastmnitSGFD-RIFGPTFIYLNkdgdlhnlyDDAKSYA 336 Cryptococcus neoformans var. neoforman...
Q5AZ85       267 G-----IIYNYIVSNHHgegtpnitNGFD-RTFGPQFYLFN---------GGGSSSL 308 Emericella nidulans
CBY00247     260 G-----IVYNYLVSNHHgngvpemvNGFD-RTFGPQYYYFN---------KGAKGTS 301 blackleg of rapeseed fungus
CBX93397     339 G-----IVYNYMVSNHHgnqvpnitNGFD-RTFGPQYYHFNk--------GGSLDQL 381 blackleg of rapeseed fungus
ADU33331     238 Qe---cLVANYFLSGHFgtpglsasPGWT-HIYGPFLLYFP---------TGDDGSI 281 mountain pine beetle
ADU33329     235 Qd---sLIANYFVSSHFgtsglsapSGWT-HIYGPWLIYFN---------TGSDSAI 278 mountain pine beetle
YP_004455650 226 Yd---gIILNYLTGAHFgtgnfqlpKHWE-KFYGPWCIYLN---------QGEQKIS 269 Melissococcus plutonius ATCC 35311

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