NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|240256053|ref|NP_567703|]
View 

Rhamnogalacturonate lyase family protein [Arabidopsis thaliana]

Protein Classification

peptidase associated/transthyretin-like domain-containing protein; TonB-dependent receptor( domain architecture ID 11161642)

peptidase associated/transthyretin-like domain-containing protein| TonB dependent receptor having a carboxypeptidase regulatory-like domain, may act as a channel to allow import of extracellular nutrients, such as iron-siderophore complexes or non-Fe compounds

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Rhamnogal_lyase pfam06045
Rhamnogalacturonate lyase family; Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the ...
 2-204 2.29e-119

Rhamnogalacturonate lyase family; Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the rhamnogalacturonan I (RG-I) backbone of pectin. This family contains mainly members from plants, but also contains the plant pathogen Erwinia chrysanthemi.


:

Pssm-ID: 283658  Cd Length: 211  Bit Score: 353.79  E-value: 2.29e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053    2 SNQDSVQLDVQESHVVMGNGKVKVTISKPDGFVTGISYQGVDNLLETHNEDFNRGYWDLVWSDEGTPGttGKSERIKGTS 81
Cdd:pfam06045  11 GGQAGVSLKVQLRYVVVDNGIVEVTFSNPDGLVTGIKYNGVDNLLEILNKIDNRGYWDLVWSKPGERT--GKTDVIKGTK 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053   82 FEVVVENEELVEISFSRKWDSSLQDSIAPINVDKRFIMRKDVTGFYSYAIFEHLAEWPAFNLPQTRIVYKLRKDKFKYMA 161
Cdd:pfam06045  89 FEIVYQNEEQIEISFSRTWDPSLRGSAVPLNVDKRFIIRRGVSGFYMYAILEHLEGWPDFDLDQTRIVFKLRKDKFDYMA 168

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 240256053  162 IADNRQRKMPLPEDRLGKRGRPLAYPEAVLLVHPVEDEFKGEV 204
Cdd:pfam06045 169 IADNRQRIMPMPEDRVPPRGQPLAYPEAVLLVNPINPMLKGEV 211
CBM-like pfam14683
Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase ...
 445-636 9.01e-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: 202.43  E-value: 9.01e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053  445 TVWEIGIPDRSAAEFFVPDPNPKYinklYIGHPDrfrqyglwerytelypkEDLVFTIGVSDYkKDWFFAHVTRKmgddt 524
Cdd:pfam14683   1 TLWQIGDPDRTAAGFLNADPNYKN----YRMHPS-----------------DDLTYTVGTSDY-SDWFFAQVNRG----- 53

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053  525 yqktTWQIKFKLENVQKSCTYKIRIALATANV-AELQVRMNDddteKTTPIFTTGVIGHDNAIARHGIH-GIYRLYNVDV 602
Cdd:pfam14683  54 ----TWTIKFTLDSVQAAGAATLRIALAGAFAgGRLQVRVNG----WTGNLPAAPTIGDSRGITRGGIYrGLYRLYEFDI 125

                         170       180       190
                  ....*....|....*....|....*....|....
gi 240256053  603 PSEKLVEGDNTLFLTQtMTTTGAFNGLMYDYIRL 636
Cdd:pfam14683 126 PASLLVAGENTITLTV-IRFLSPFRGVMYDYIRL 158
RGL4_M cd10316
Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 336-435 4.31e-32

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: 119.28  E-value: 4.31e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053 336 KRGCISGRLLVCDKflsddfLPANGAFVGLAPPGEVGSwQLESKGYQFWTEADSDGYFAINDIREGEYNLNGYVTGWIGD 415
Cdd:cd10316    1 GRGTVSGRLLLPDG------ASAAIAVVGLANPGEQGS-QFETKGYQYWTEADSDGRFTIPNVRPGTYRLTAYADGIFGY 73

                         90       100
                 ....*....|....*....|
gi 240256053 416 YqYEQLINITAGCDIDVGNI 435
Cdd:cd10316   74 V-AQDTVTVTAGGTTALGDL 92
 
Name Accession Description Interval E-value
Rhamnogal_lyase pfam06045
Rhamnogalacturonate lyase family; Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the ...
 2-204 2.29e-119

Rhamnogalacturonate lyase family; Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the rhamnogalacturonan I (RG-I) backbone of pectin. This family contains mainly members from plants, but also contains the plant pathogen Erwinia chrysanthemi.


Pssm-ID: 283658  Cd Length: 211  Bit Score: 353.79  E-value: 2.29e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053    2 SNQDSVQLDVQESHVVMGNGKVKVTISKPDGFVTGISYQGVDNLLETHNEDFNRGYWDLVWSDEGTPGttGKSERIKGTS 81
Cdd:pfam06045  11 GGQAGVSLKVQLRYVVVDNGIVEVTFSNPDGLVTGIKYNGVDNLLEILNKIDNRGYWDLVWSKPGERT--GKTDVIKGTK 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053   82 FEVVVENEELVEISFSRKWDSSLQDSIAPINVDKRFIMRKDVTGFYSYAIFEHLAEWPAFNLPQTRIVYKLRKDKFKYMA 161
Cdd:pfam06045  89 FEIVYQNEEQIEISFSRTWDPSLRGSAVPLNVDKRFIIRRGVSGFYMYAILEHLEGWPDFDLDQTRIVFKLRKDKFDYMA 168

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 240256053  162 IADNRQRKMPLPEDRLGKRGRPLAYPEAVLLVHPVEDEFKGEV 204
Cdd:pfam06045 169 IADNRQRIMPMPEDRVPPRGQPLAYPEAVLLVNPINPMLKGEV 211
RGL4_N cd10320
N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 14-295 2.38e-74

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: 239.60  E-value: 2.38e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053  14 SHVVMGNGKVKVTISKPDGFVTGISYQGvdnLLETHNEDFNRGYWDLVWSDEG-TPGTTGKSERIKGTSFEVVVENEELV 92
Cdd:cd10320    8 SAVVVDNGLLGLVFSVDGGIVTGILYGG---LLENDNGKGDRGYLDLVSIVYGgTEQTPGKLSHIESGLGATVSATQSGD 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053  93 EI--SFSRkwdsslqdsiaPINVDKRFIMRKDVTGFYSYAIFEHLAewPAFNLPQTRIVYKLRKDKFKYMAIADnRQRKM 170
Cdd:cd10320   85 YIqiSFSR-----------TFETELHYVVRKGEPGIYMYTVATHPA--PEPSLGELRTVFRLNPDLFPNGAISD-DRGDP 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053 171 PLPEDrlgkrgrpLAYPEAVLLVHPVEDefkGEVDDKYEYSSENKDLKVHGWISHnlDLGCWQIIPSNEFRSGGLSKQNL 250
Cdd:cd10320  151 PPGTA--------LEGKEVQDDTFPLPD---GEYDSKYYYSGYNRDNKVHGVYGD--GVGAWMIMPSREYSSGGPLKQDL 217

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 240256053 251 TSHVGPISLAMFLSAHYAGEDMVmkvkAGDSWKKVFGPVFTYLNC 295
Cdd:cd10320  218 TVHGGPILLNYFNSGHYGGKDLN----ATEGWRKLFGPYLLYFNS 258
CBM-like pfam14683
Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase ...
 445-636 9.01e-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: 202.43  E-value: 9.01e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053  445 TVWEIGIPDRSAAEFFVPDPNPKYinklYIGHPDrfrqyglwerytelypkEDLVFTIGVSDYkKDWFFAHVTRKmgddt 524
Cdd:pfam14683   1 TLWQIGDPDRTAAGFLNADPNYKN----YRMHPS-----------------DDLTYTVGTSDY-SDWFFAQVNRG----- 53

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053  525 yqktTWQIKFKLENVQKSCTYKIRIALATANV-AELQVRMNDddteKTTPIFTTGVIGHDNAIARHGIH-GIYRLYNVDV 602
Cdd:pfam14683  54 ----TWTIKFTLDSVQAAGAATLRIALAGAFAgGRLQVRVNG----WTGNLPAAPTIGDSRGITRGGIYrGLYRLYEFDI 125

                         170       180       190
                  ....*....|....*....|....*....|....
gi 240256053  603 PSEKLVEGDNTLFLTQtMTTTGAFNGLMYDYIRL 636
Cdd:pfam14683 126 PASLLVAGENTITLTV-IRFLSPFRGVMYDYIRL 158
RGL4_C cd10317
C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 447-637 2.60e-52

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: 177.47  E-value: 2.60e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053 447 WEIGIPDRSAAEFFVPDPNPKYINKlyighpdrfrqyglwerYTELYPKEDLVFTIGVSDYKKDWFFAHVtrkmgddtyQ 526
Cdd:cd10317    1 WQIGTPDRTAAEFRNGDLLPNYHPS-----------------DWRLAPPGDLTYTVGSSDSDFDWYYAQS---------V 54

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053 527 KTTWQIKFKLENVQKSCTYKIRIALATA-NVAELQVRMNDDdtektTPIFTTGVIGHD-NAIARHGIHGIYRLYNVDVPS 604
Cdd:cd10317   55 NGPWTIRFDLTAVQATGGATLRIALAGAsAGGRPQVRVNDN-----GPLLPTAPTGNDsRGIYRGAYRGNYHLYEFDIPA 129

                        170       180       190
                 ....*....|....*....|....*....|...
gi 240256053 605 EKLVEGDNTLFLTQTmTTTGAFNGLMYDYIRLE 637
Cdd:cd10317  130 SLLVAGTNTITLTVV-SGSSLSPGVMYDAIRLE 161
RGL4_M cd10316
Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 336-435 4.31e-32

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: 119.28  E-value: 4.31e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053 336 KRGCISGRLLVCDKflsddfLPANGAFVGLAPPGEVGSwQLESKGYQFWTEADSDGYFAINDIREGEYNLNGYVTGWIGD 415
Cdd:cd10316    1 GRGTVSGRLLLPDG------ASAAIAVVGLANPGEQGS-QFETKGYQYWTEADSDGRFTIPNVRPGTYRLTAYADGIFGY 73

                         90       100
                 ....*....|....*....|
gi 240256053 416 YqYEQLINITAGCDIDVGNI 435
Cdd:cd10316   74 V-AQDTVTVTAGGTTALGDL 92
fn3_3 pfam14686
Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase ...
 358-431 5.63e-25

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: 98.43  E-value: 5.63e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 240256053  358 ANGAFVGLAPP-GEVGSWQLESKGYQFWTEADSDGYFAINDIREGEYNLNGYVTGWIGDYQyEQLINITAGCDID 431
Cdd:pfam14686   1 GRGAVSGLAVGsGDVVSWQNESKGYQYWTRADSSGSFTIPNVRPGTYRLTAYADGLFGDYK-QDDVTVSAGSTTT 74
 
Name Accession Description Interval E-value
Rhamnogal_lyase pfam06045
Rhamnogalacturonate lyase family; Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the ...
 2-204 2.29e-119

Rhamnogalacturonate lyase family; Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the rhamnogalacturonan I (RG-I) backbone of pectin. This family contains mainly members from plants, but also contains the plant pathogen Erwinia chrysanthemi.


Pssm-ID: 283658  Cd Length: 211  Bit Score: 353.79  E-value: 2.29e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053    2 SNQDSVQLDVQESHVVMGNGKVKVTISKPDGFVTGISYQGVDNLLETHNEDFNRGYWDLVWSDEGTPGttGKSERIKGTS 81
Cdd:pfam06045  11 GGQAGVSLKVQLRYVVVDNGIVEVTFSNPDGLVTGIKYNGVDNLLEILNKIDNRGYWDLVWSKPGERT--GKTDVIKGTK 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053   82 FEVVVENEELVEISFSRKWDSSLQDSIAPINVDKRFIMRKDVTGFYSYAIFEHLAEWPAFNLPQTRIVYKLRKDKFKYMA 161
Cdd:pfam06045  89 FEIVYQNEEQIEISFSRTWDPSLRGSAVPLNVDKRFIIRRGVSGFYMYAILEHLEGWPDFDLDQTRIVFKLRKDKFDYMA 168

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 240256053  162 IADNRQRKMPLPEDRLGKRGRPLAYPEAVLLVHPVEDEFKGEV 204
Cdd:pfam06045 169 IADNRQRIMPMPEDRVPPRGQPLAYPEAVLLVNPINPMLKGEV 211
RGL4_N cd10320
N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 14-295 2.38e-74

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: 239.60  E-value: 2.38e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053  14 SHVVMGNGKVKVTISKPDGFVTGISYQGvdnLLETHNEDFNRGYWDLVWSDEG-TPGTTGKSERIKGTSFEVVVENEELV 92
Cdd:cd10320    8 SAVVVDNGLLGLVFSVDGGIVTGILYGG---LLENDNGKGDRGYLDLVSIVYGgTEQTPGKLSHIESGLGATVSATQSGD 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053  93 EI--SFSRkwdsslqdsiaPINVDKRFIMRKDVTGFYSYAIFEHLAewPAFNLPQTRIVYKLRKDKFKYMAIADnRQRKM 170
Cdd:cd10320   85 YIqiSFSR-----------TFETELHYVVRKGEPGIYMYTVATHPA--PEPSLGELRTVFRLNPDLFPNGAISD-DRGDP 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053 171 PLPEDrlgkrgrpLAYPEAVLLVHPVEDefkGEVDDKYEYSSENKDLKVHGWISHnlDLGCWQIIPSNEFRSGGLSKQNL 250
Cdd:cd10320  151 PPGTA--------LEGKEVQDDTFPLPD---GEYDSKYYYSGYNRDNKVHGVYGD--GVGAWMIMPSREYSSGGPLKQDL 217

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 240256053 251 TSHVGPISLAMFLSAHYAGEDMVmkvkAGDSWKKVFGPVFTYLNC 295
Cdd:cd10320  218 TVHGGPILLNYFNSGHYGGKDLN----ATEGWRKLFGPYLLYFNS 258
CBM-like pfam14683
Polysaccharide lyase family 4, domain III; CBM-like is domain III of rhamnogalacturonan lyase ...
 445-636 9.01e-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: 202.43  E-value: 9.01e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053  445 TVWEIGIPDRSAAEFFVPDPNPKYinklYIGHPDrfrqyglwerytelypkEDLVFTIGVSDYkKDWFFAHVTRKmgddt 524
Cdd:pfam14683   1 TLWQIGDPDRTAAGFLNADPNYKN----YRMHPS-----------------DDLTYTVGTSDY-SDWFFAQVNRG----- 53

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053  525 yqktTWQIKFKLENVQKSCTYKIRIALATANV-AELQVRMNDddteKTTPIFTTGVIGHDNAIARHGIH-GIYRLYNVDV 602
Cdd:pfam14683  54 ----TWTIKFTLDSVQAAGAATLRIALAGAFAgGRLQVRVNG----WTGNLPAAPTIGDSRGITRGGIYrGLYRLYEFDI 125

                         170       180       190
                  ....*....|....*....|....*....|....
gi 240256053  603 PSEKLVEGDNTLFLTQtMTTTGAFNGLMYDYIRL 636
Cdd:pfam14683 126 PASLLVAGENTITLTV-IRFLSPFRGVMYDYIRL 158
RGL4_C cd10317
C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 447-637 2.60e-52

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: 177.47  E-value: 2.60e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053 447 WEIGIPDRSAAEFFVPDPNPKYINKlyighpdrfrqyglwerYTELYPKEDLVFTIGVSDYKKDWFFAHVtrkmgddtyQ 526
Cdd:cd10317    1 WQIGTPDRTAAEFRNGDLLPNYHPS-----------------DWRLAPPGDLTYTVGSSDSDFDWYYAQS---------V 54

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053 527 KTTWQIKFKLENVQKSCTYKIRIALATA-NVAELQVRMNDDdtektTPIFTTGVIGHD-NAIARHGIHGIYRLYNVDVPS 604
Cdd:cd10317   55 NGPWTIRFDLTAVQATGGATLRIALAGAsAGGRPQVRVNDN-----GPLLPTAPTGNDsRGIYRGAYRGNYHLYEFDIPA 129

                        170       180       190
                 ....*....|....*....|....*....|...
gi 240256053 605 EKLVEGDNTLFLTQTmTTTGAFNGLMYDYIRLE 637
Cdd:cd10317  130 SLLVAGTNTITLTVV-SGSSLSPGVMYDAIRLE 161
RGL4_M cd10316
Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase; The ...
 336-435 4.31e-32

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: 119.28  E-value: 4.31e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256053 336 KRGCISGRLLVCDKflsddfLPANGAFVGLAPPGEVGSwQLESKGYQFWTEADSDGYFAINDIREGEYNLNGYVTGWIGD 415
Cdd:cd10316    1 GRGTVSGRLLLPDG------ASAAIAVVGLANPGEQGS-QFETKGYQYWTEADSDGRFTIPNVRPGTYRLTAYADGIFGY 73

                         90       100
                 ....*....|....*....|
gi 240256053 416 YqYEQLINITAGCDIDVGNI 435
Cdd:cd10316   74 V-AQDTVTVTAGGTTALGDL 92
fn3_3 pfam14686
Polysaccharide lyase family 4, domain II; FnIII-like is domain II of rhamnogalacturonan lyase ...
 358-431 5.63e-25

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: 98.43  E-value: 5.63e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 240256053  358 ANGAFVGLAPP-GEVGSWQLESKGYQFWTEADSDGYFAINDIREGEYNLNGYVTGWIGDYQyEQLINITAGCDID 431
Cdd:pfam14686   1 GRGAVSGLAVGsGDVVSWQNESKGYQYWTRADSSGSFTIPNVRPGTYRLTAYADGLFGDYK-QDDVTVSAGSTTT 74
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH