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Conserved domains on  [gi|67541943|ref|XP_664739|]
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rhamnogalacturonate lyase B [Aspergillus nidulans FGSC A4]

Protein Classification

RGL4_N and RGL4_C domain-containing protein( domain architecture ID 11182470)

protein containing domains RGL4_N, RGL4_M, and RGL4_C

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RhgB_N pfam09284
Rhamnogalacturonan lyase B, N-terminal; Members of this family are found in both fungi, ...
 24-270 2.36e-145

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).


:

Pssm-ID: 462742  Cd Length: 249  Bit Score: 417.36  E-value: 2.36e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943    24 ITDNGSSYTIDANSPnpLKFTVNKSSCDITSIVYYGSEFQYSGKGSHIGSGLGSATVSATQSGD-YIKVTCDTSSLTHYF 102
Cdd:pfam09284   1 YTDSGSNYVVDTGSG--LVFTVSKSNGDITSIKYNGTEYQYSSKGSHIESGLGSATVTIETIGDsYIKVTCTTGTLTHYY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943   103 VVHNGDPIIHMATYITAEPDIGELRFIARLNSNLLPNEePFGDVSTTSGG-SAIEGSDVFLVNGETRSKFYSSERFIDDH 181
Cdd:pfam09284  79 VARYGENNIYMATYITAEPSVGELRFIARLNRSILPNG-PFGDVSTTDGGtSAIEGSDVFVVNGQTRSKFYSSQRFIDDD 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943   182 RHCISGSAHRVCMILN--QYESSSGGPFFRDINSNNGGDYNALYWYMNSGHVQTESFRTGLHGPYSMYFSRSGTPSTNI- 258
Cdd:pfam09284 158 VHGVTGSAVGVCMIRPgsNYEKSSGGPFFRDINNNNGGDYTELYFYMNSGHVQTESYRMGLHGPYALTFTRGGAPSASLl 237

                         250
                  ....*....|..
gi 67541943   259 DTSFFASLGIKG 270
Cdd:pfam09284 238 DTSFFDDLGIKG 249
CBM-like pfam14683
Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase ...
 361-525 6.10e-62

Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain possesses a jelly roll beta-sandwich fold structurally homologous to carbohydrate binding modules (CBMs), and it carries two sulfate ions and a hexa-coordinated calcium ion.


:

Pssm-ID: 464260  Cd Length: 158  Bit Score: 200.12  E-value: 6.10e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943   361 TIFKIGEWDGQPTGFRNAD---KQLRMHPSDSRmdswssTYTVGSSSLSDFpmaVFKSVNN-PVTIKFTATSAQ-TGAAT 435
Cdd:pfam14683   1 TLWQIGDPDRTAAGFLNADpnyKNYRMHPSDDL------TYTVGTSDYSDW---FFAQVNRgTWTIKFTLDSVQaAGAAT 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943   436 LRIGTTLSFAGGRPQATINSYTGPAPSAPTNLNSRGVTRGA-YRGLGEVYDVSVPAGTIVTGENTITISVISgssgdaFL 514
Cdd:pfam14683  72 LRIALAGAFAGGRLQVRVNGWTGNLPAAPTIGDSRGITRGGiYRGLYRLYEFDIPASLLVAGENTITLTVIR------FL 145

                         170
                  ....*....|...
gi 67541943   515 SP--NVVFDCIEL 525
Cdd:pfam14683 146 SPfrGVMYDYIRL 158
fn3_3 pfam14686
Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase ...
 276-349 7.96e-23

Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal beta-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits.


:

Pssm-ID: 464261  Cd Length: 74  Bit Score: 91.88  E-value: 7.96e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 67541943   276 GRGTVTGKASGADSsmdwVVHWYNN--DAQYWTYTASDGSFTSPAMKPGTYTMKYYQGEFPVA--ETTVTVSAGSSTT 349
Cdd:pfam14686   1 GRGAVSGLAVGSGD----VVSWQNEskGYQYWTRADSSGSFTIPNVRPGTYRLTAYADGLFGDykQDDVTVSAGSTTT 74
 
Name Accession Description Interval E-value
RhgB_N pfam09284
Rhamnogalacturonan lyase B, N-terminal; Members of this family are found in both fungi, ...
 24-270 2.36e-145

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).


Pssm-ID: 462742  Cd Length: 249  Bit Score: 417.36  E-value: 2.36e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943    24 ITDNGSSYTIDANSPnpLKFTVNKSSCDITSIVYYGSEFQYSGKGSHIGSGLGSATVSATQSGD-YIKVTCDTSSLTHYF 102
Cdd:pfam09284   1 YTDSGSNYVVDTGSG--LVFTVSKSNGDITSIKYNGTEYQYSSKGSHIESGLGSATVTIETIGDsYIKVTCTTGTLTHYY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943   103 VVHNGDPIIHMATYITAEPDIGELRFIARLNSNLLPNEePFGDVSTTSGG-SAIEGSDVFLVNGETRSKFYSSERFIDDH 181
Cdd:pfam09284  79 VARYGENNIYMATYITAEPSVGELRFIARLNRSILPNG-PFGDVSTTDGGtSAIEGSDVFVVNGQTRSKFYSSQRFIDDD 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943   182 RHCISGSAHRVCMILN--QYESSSGGPFFRDINSNNGGDYNALYWYMNSGHVQTESFRTGLHGPYSMYFSRSGTPSTNI- 258
Cdd:pfam09284 158 VHGVTGSAVGVCMIRPgsNYEKSSGGPFFRDINNNNGGDYTELYFYMNSGHVQTESYRMGLHGPYALTFTRGGAPSASLl 237

                         250
                  ....*....|..
gi 67541943   259 DTSFFASLGIKG 270
Cdd:pfam09284 238 DTSFFDDLGIKG 249
CBM-like pfam14683
Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase ...
 361-525 6.10e-62

Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain possesses a jelly roll beta-sandwich fold structurally homologous to carbohydrate binding modules (CBMs), and it carries two sulfate ions and a hexa-coordinated calcium ion.


Pssm-ID: 464260  Cd Length: 158  Bit Score: 200.12  E-value: 6.10e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943   361 TIFKIGEWDGQPTGFRNAD---KQLRMHPSDSRmdswssTYTVGSSSLSDFpmaVFKSVNN-PVTIKFTATSAQ-TGAAT 435
Cdd:pfam14683   1 TLWQIGDPDRTAAGFLNADpnyKNYRMHPSDDL------TYTVGTSDYSDW---FFAQVNRgTWTIKFTLDSVQaAGAAT 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943   436 LRIGTTLSFAGGRPQATINSYTGPAPSAPTNLNSRGVTRGA-YRGLGEVYDVSVPAGTIVTGENTITISVISgssgdaFL 514
Cdd:pfam14683  72 LRIALAGAFAGGRLQVRVNGWTGNLPAAPTIGDSRGITRGGiYRGLYRLYEFDIPASLLVAGENTITLTVIR------FL 145

                         170
                  ....*....|...
gi 67541943   515 SP--NVVFDCIEL 525
Cdd:pfam14683 146 SPfrGVMYDYIRL 158
RGL4_N cd10320
N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 22-256 7.95e-60

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.


Pssm-ID: 199907 [Multi-domain]  Cd Length: 265  Bit Score: 198.38  E-value: 7.95e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943  22 FGITDNGSSYTIDaNSPNPLKFTVNK---------------------SSCDITSIVYYGSEfQYSGKGSHIGSGLGsATV 80
Cdd:cd10320   1 FGLTDSGSAVVVD-NGLLGLVFSVDGgivtgilyggllendngkgdrGYLDLVSIVYGGTE-QTPGKLSHIESGLG-ATV 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943  81 SATQSGDYIKVTC-DTSSLTHYFVVHNGDPIIHMATYITA---EPDIGELRFIARLNSNLLPNEEPFGDVSTTSGGSAIE 156
Cdd:cd10320  78 SATQSGDYIQISFsRTFETELHYVVRKGEPGIYMYTVATHpapEPSLGELRTVFRLNPDLFPNGAISDDRGDPPPGTALE 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943 157 G----SDVFLVN-GETRSKFYSSERFIDDHRHCISGSAHRVCMILNQYESSSGGPFFRDINSNNGgdyNALYWYMNSGHV 231
Cdd:cd10320 158 GkevqDDTFPLPdGEYDSKYYYSGYNRDNKVHGVYGDGVGAWMIMPSREYSSGGPLKQDLTVHGG---PILLNYFNSGHY 234

                       250       260       270
                ....*....|....*....|....*....|
gi 67541943 232 QTESFR-----TGLHGPYSMYFSRSGTPST 256
Cdd:cd10320 235 GGKDLNategwRKLFGPYLLYFNSGGAPST 264
RGL4_C cd10317
C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 363-526 1.85e-58

C-terminal 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. Both the middle and the C-terminal domain are 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.


Pssm-ID: 199905  Cd Length: 161  Bit Score: 191.33  E-value: 1.85e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943 363 FKIGEWDGQPTGFRNADKQLRMHPSDSRMDSWSS-TYTVGSSSlSDFPMAVFKSVNNPVTIKFTATSAQ-TGAATLRIGT 440
Cdd:cd10317   1 WQIGTPDRTAAEFRNGDLLPNYHPSDWRLAPPGDlTYTVGSSD-SDFDWYYAQSVNGPWTIRFDLTAVQaTGGATLRIAL 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943 441 TLSFAGGRPQATINSYTGPAPSAPTNLNSRGVTRGAYRGLGEVYDVSVPAGTIVTGENTITISVISGSSgdafLSPNVVF 520
Cdd:cd10317  80 AGASAGGRPQVRVNDNGPLLPTAPTGNDSRGIYRGAYRGNYHLYEFDIPASLLVAGTNTITLTVVSGSS----LSPGVMY 155


                ....*.
gi 67541943 521 DCIELF 526
Cdd:cd10317 156 DAIRLE 161
fn3_3 pfam14686
Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase ...
 276-349 7.96e-23

Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal beta-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits.


Pssm-ID: 464261  Cd Length: 74  Bit Score: 91.88  E-value: 7.96e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 67541943   276 GRGTVTGKASGADSsmdwVVHWYNN--DAQYWTYTASDGSFTSPAMKPGTYTMKYYQGEFPVA--ETTVTVSAGSSTT 349
Cdd:pfam14686   1 GRGAVSGLAVGSGD----VVSWQNEskGYQYWTRADSSGSFTIPNVRPGTYRLTAYADGLFGDykQDDVTVSAGSTTT 74
RGL4_M cd10316
Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 276-349 7.32e-17

Middle 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. Both the middle domain represented by this model and the C-terminal domain are 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.


Pssm-ID: 199904  Cd Length: 92  Bit Score: 75.75  E-value: 7.32e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943 276 GRGTVTGKASGAD--SSMDWVVHWYNND----------AQYWTYTASDGSFTSPAMKPGTYTMKYYQGEFP--VAETTVT 341
Cdd:cd10316   1 GRGTVSGRLLLPDgaSAAIAVVGLANPGeqgsqfetkgYQYWTEADSDGRFTIPNVRPGTYRLTAYADGIFgyVAQDTVT 80


                ....*...
gi 67541943 342 VSAGSSTT 349
Cdd:cd10316  81 VTAGGTTA 88
 
Name Accession Description Interval E-value
RhgB_N pfam09284
Rhamnogalacturonan lyase B, N-terminal; Members of this family are found in both fungi, ...
 24-270 2.36e-145

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).


Pssm-ID: 462742  Cd Length: 249  Bit Score: 417.36  E-value: 2.36e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943    24 ITDNGSSYTIDANSPnpLKFTVNKSSCDITSIVYYGSEFQYSGKGSHIGSGLGSATVSATQSGD-YIKVTCDTSSLTHYF 102
Cdd:pfam09284   1 YTDSGSNYVVDTGSG--LVFTVSKSNGDITSIKYNGTEYQYSSKGSHIESGLGSATVTIETIGDsYIKVTCTTGTLTHYY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943   103 VVHNGDPIIHMATYITAEPDIGELRFIARLNSNLLPNEePFGDVSTTSGG-SAIEGSDVFLVNGETRSKFYSSERFIDDH 181
Cdd:pfam09284  79 VARYGENNIYMATYITAEPSVGELRFIARLNRSILPNG-PFGDVSTTDGGtSAIEGSDVFVVNGQTRSKFYSSQRFIDDD 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943   182 RHCISGSAHRVCMILN--QYESSSGGPFFRDINSNNGGDYNALYWYMNSGHVQTESFRTGLHGPYSMYFSRSGTPSTNI- 258
Cdd:pfam09284 158 VHGVTGSAVGVCMIRPgsNYEKSSGGPFFRDINNNNGGDYTELYFYMNSGHVQTESYRMGLHGPYALTFTRGGAPSASLl 237

                         250
                  ....*....|..
gi 67541943   259 DTSFFASLGIKG 270
Cdd:pfam09284 238 DTSFFDDLGIKG 249
CBM-like pfam14683
Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase ...
 361-525 6.10e-62

Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain possesses a jelly roll beta-sandwich fold structurally homologous to carbohydrate binding modules (CBMs), and it carries two sulfate ions and a hexa-coordinated calcium ion.


Pssm-ID: 464260  Cd Length: 158  Bit Score: 200.12  E-value: 6.10e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943   361 TIFKIGEWDGQPTGFRNAD---KQLRMHPSDSRmdswssTYTVGSSSLSDFpmaVFKSVNN-PVTIKFTATSAQ-TGAAT 435
Cdd:pfam14683   1 TLWQIGDPDRTAAGFLNADpnyKNYRMHPSDDL------TYTVGTSDYSDW---FFAQVNRgTWTIKFTLDSVQaAGAAT 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943   436 LRIGTTLSFAGGRPQATINSYTGPAPSAPTNLNSRGVTRGA-YRGLGEVYDVSVPAGTIVTGENTITISVISgssgdaFL 514
Cdd:pfam14683  72 LRIALAGAFAGGRLQVRVNGWTGNLPAAPTIGDSRGITRGGiYRGLYRLYEFDIPASLLVAGENTITLTVIR------FL 145

                         170
                  ....*....|...
gi 67541943   515 SP--NVVFDCIEL 525
Cdd:pfam14683 146 SPfrGVMYDYIRL 158
RGL4_N cd10320
N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 22-256 7.95e-60

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.


Pssm-ID: 199907 [Multi-domain]  Cd Length: 265  Bit Score: 198.38  E-value: 7.95e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943  22 FGITDNGSSYTIDaNSPNPLKFTVNK---------------------SSCDITSIVYYGSEfQYSGKGSHIGSGLGsATV 80
Cdd:cd10320   1 FGLTDSGSAVVVD-NGLLGLVFSVDGgivtgilyggllendngkgdrGYLDLVSIVYGGTE-QTPGKLSHIESGLG-ATV 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943  81 SATQSGDYIKVTC-DTSSLTHYFVVHNGDPIIHMATYITA---EPDIGELRFIARLNSNLLPNEEPFGDVSTTSGGSAIE 156
Cdd:cd10320  78 SATQSGDYIQISFsRTFETELHYVVRKGEPGIYMYTVATHpapEPSLGELRTVFRLNPDLFPNGAISDDRGDPPPGTALE 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943 157 G----SDVFLVN-GETRSKFYSSERFIDDHRHCISGSAHRVCMILNQYESSSGGPFFRDINSNNGgdyNALYWYMNSGHV 231
Cdd:cd10320 158 GkevqDDTFPLPdGEYDSKYYYSGYNRDNKVHGVYGDGVGAWMIMPSREYSSGGPLKQDLTVHGG---PILLNYFNSGHY 234

                       250       260       270
                ....*....|....*....|....*....|
gi 67541943 232 QTESFR-----TGLHGPYSMYFSRSGTPST 256
Cdd:cd10320 235 GGKDLNategwRKLFGPYLLYFNSGGAPST 264
RGL4_C cd10317
C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 363-526 1.85e-58

C-terminal 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. Both the middle and the C-terminal domain are 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.


Pssm-ID: 199905  Cd Length: 161  Bit Score: 191.33  E-value: 1.85e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943 363 FKIGEWDGQPTGFRNADKQLRMHPSDSRMDSWSS-TYTVGSSSlSDFPMAVFKSVNNPVTIKFTATSAQ-TGAATLRIGT 440
Cdd:cd10317   1 WQIGTPDRTAAEFRNGDLLPNYHPSDWRLAPPGDlTYTVGSSD-SDFDWYYAQSVNGPWTIRFDLTAVQaTGGATLRIAL 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943 441 TLSFAGGRPQATINSYTGPAPSAPTNLNSRGVTRGAYRGLGEVYDVSVPAGTIVTGENTITISVISGSSgdafLSPNVVF 520
Cdd:cd10317  80 AGASAGGRPQVRVNDNGPLLPTAPTGNDSRGIYRGAYRGNYHLYEFDIPASLLVAGTNTITLTVVSGSS----LSPGVMY 155


                ....*.
gi 67541943 521 DCIELF 526
Cdd:cd10317 156 DAIRLE 161
fn3_3 pfam14686
Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase ...
 276-349 7.96e-23

Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal beta-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits.


Pssm-ID: 464261  Cd Length: 74  Bit Score: 91.88  E-value: 7.96e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 67541943   276 GRGTVTGKASGADSsmdwVVHWYNN--DAQYWTYTASDGSFTSPAMKPGTYTMKYYQGEFPVA--ETTVTVSAGSSTT 349
Cdd:pfam14686   1 GRGAVSGLAVGSGD----VVSWQNEskGYQYWTRADSSGSFTIPNVRPGTYRLTAYADGLFGDykQDDVTVSAGSTTT 74
RGL4_M cd10316
Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 276-349 7.32e-17

Middle 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. Both the middle domain represented by this model and the C-terminal domain are 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.


Pssm-ID: 199904  Cd Length: 92  Bit Score: 75.75  E-value: 7.32e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67541943 276 GRGTVTGKASGAD--SSMDWVVHWYNND----------AQYWTYTASDGSFTSPAMKPGTYTMKYYQGEFP--VAETTVT 341
Cdd:cd10316   1 GRGTVSGRLLLPDgaSAAIAVVGLANPGeqgsqfetkgYQYWTEADSDGRFTIPNVRPGTYRLTAYADGIFgyVAQDTVT 80


                ....*...
gi 67541943 342 VSAGSSTT 349
Cdd:cd10316  81 VTAGGTTA 88
CarboxypepD_reg pfam13620
Carboxypeptidase regulatory-like domain;
299-352 7.97e-03

Carboxypeptidase regulatory-like domain;


Pssm-ID: 433354 [Multi-domain]  Cd Length: 81  Bit Score: 35.72  E-value: 7.97e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 67541943   299 NNDAQYWTYTASDGSFTSPAMKPGTYTMK-YYQGEFPVAETTVTVSAGSSTTKNI 352
Cdd:pfam13620  25 DTGTVRTTTTDADGRYRFPGLPPGTYTVTvSAPGFKTATRTGVTVTAGQTTTLDV 79
 
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.
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