4RUB,1BXN,1GEH,1IWA,1RSC,1RUS,1SVD,2CWX,9RUB


Conserved Protein Domain Family
RuBisCO_large_I_II_III

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cd08206: RuBisCO_large_I_II_III 
Click on image for an interactive view with Cn3D
Ribulose bisphosphate carboxylase large chain, Form I,II,III
Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubico-like proteins (RLP), are missing critical active site residues.
Statistics
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PSSM-Id: 173971
View PSSM: cd08206
Aligned: 36 rows
Threshold Bit Score: 488.284
Threshold Setting Gi: 75282237
Created: 4-Jan-2010
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 19 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:4RUB, Nicotiana tabacum ribulose-1,5-bisphosphate carboxylase/oxygenase with bound magnesium and transition analog , contacts 4A
    View structure with Cn3D
  • Citation:PMID 3681999

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                  #    ##                                               
4RUB_A        34 TDILAAFRVTpqpGVPPEEAGAAVAAESSTGTWTtvwtdgltsldRYKGRCYRIervvg----ekdqyIAYVAYPLDLFE 109 common tobacco
1RUS_B        46 EHVLCAYIMKpkaGYGYVATAAHFAAESSTGTNVevctt-ddftrGVDALVYEVdea---------reLTKIAYPVALFD 115 Rhodospirillum ...
9RUB_A        22 EHVLCAYIMKpkaGYGYVATAAHFAAESSTGTNVevctt-ddftrGVDALVYEVdea---------reLTKIAYPVALFD 91  Rhodospirillum ...
Q58632        13 GDLLSCMVIK---GENLEKLANEIAGESSIGTWTkvqtmksdiyeKLRPKVYEIkeigee--ngykvgLIKIAYPLYDFE 87  Methanocaldococ...
Q8THG2        15 TDLICEFHIEpaaGISFEEASTHMAGESSIDSWTeistlspelaaRLKPHVFYLdad---------tqTVRVAYSEDLFE 85  Methanosarcina ...
Q41407        22 EHVLVAYIMKpkmGYDYLATAAHFAAESCTGARStdd-----akeSANAVVYYIdad---------sqEMRIAYPTVLFD 87  Symbiodinium sp.
O84917        24 KHILVAYKMKpkaGYDYLATAAHFAAESSTGTNVevstt-ddftkGVDALVYFIdea---------teDMRIAYPIELFD 93  Thiomonas inter...
ZP_01451219   22 KHLLVAYKLIpakGYGFLEVAAHIAAESSTGTNVevstt-ddftrGVDALVYDIdetafgdegvtgggLMKVAYPVELFD 100 Mariprofundus f...
Q31IK3        22 NHILVAYTMEpaaGYGYLEVAAHIAAESSTGTNVevctt-ddftkGVDAIVYDIdea---------ngIMKVAYPFDLFD 91  Thiomicrospira ...
YP_003239796  16 SDCLACFYVEpaeGVDIYEAAGAVASESSIGTWTdvatmkpriweELRARVYAIeg-----------nVVKIAYPAALFE 84  Ammonifex degen...
Feature 1                           #                                                    # # #   
4RUB_A       110 e------GSVTNMFTSIVGNVFGFKaLRALRLEDLRIPPAYVKTfqGPPHGIQVERDKLNky---gRPLLGCTIKPKLGL 180 common tobacco
1RUS_B       116 rnitdgkAMIASFLTLTMGNNQGMGdVEYAKMHDFYVPEAYRALfdGPSVNISALWKVLGrpevdgGLVVGTIIKPKLGL 195 Rhodospirillum ...
9RUB_A        92 rnitdgkAMIASFLTLTMGNNQGMGdVEYAKMHDFYVPEAYRALfdGPSVNISALWKVLGrpevdgGLVVGTIIKPKLGL 171 Rhodospirillum ...
Q58632        88 i------NNMPGVLAGIAGNIFGMKiAKGLRILDFRFPAEFVKAykGPRFGIEGVRETLKik---eRPLLGTIVKPKVGL 158 Methanocaldococ...
Q8THG2        86 l------GSVPQVLSAVAGNIFSMKiVDNLRLQDITFPKSMLREfeGPNFGLPGVRDIVGvk---dRPLVGTIVKPKVGL 156 Methanosarcina ...
Q41407        88 snltdgrDMVRSFLTLAIGNTQGMEdVEFGKIYDFYLPPSFLRL--QESPSVNTMWRILDkga-snGGLAAGAMKPKLGM 164 Symbiodinium sp.
O84917        94 rnvidgrFMIVSFLTLVIGNNQGMGdVEYGKMIDFYVPERAIQMfdGPATDISNLWRILGrpikdgGYIAGTIIKPKLGL 173 Thiomonas inter...
ZP_01451219  101 pnlidghYNVSHMWSLILGNNQGMGdHEGLRMLDFMVPECMIRKfdGPSAGIADLWKVLGrpevdgGYISGTIIKPKLGL 180 Mariprofundus f...
Q31IK3        92 rngldgkTMIVSFLTLAIGNNQGMGdVKNLQMFDFWVPETKLHLfdGPAVDITNMWKMLGrdkdngGYIAGTIIKPKLGL 171 Thiomicrospira ...
YP_003239796  85 p------GNIPQYLSSIAGNIFGMKaVKNLRLLDISFPPELVSGslGPAFGVQGVRETLGiy---gRPLVGTIVKPKLGL 155 Ammonifex degen...
Feature 1                              ##                                                        
4RUB_A       181 SAKNYGRAVYECLRGGlDFTKDDEnVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGtCEEMIKRAVFAREl 260 common tobacco
1RUS_B       196 RPKPFAEACHAFWLGG-DFIKNDEpQGNQPFAPLRDTIALVADAMRRAQDETGEAKLFSANITADdPFEIIARGEYVLEt 274 Rhodospirillum ...
9RUB_A       172 RPKPFAEACHAFWLGG-DFIKNDEpQGNQPFAPLRDTIALVADAMRRAQDETGEAKLFSANITADdPFEIIARGEYVLEt 250 Rhodospirillum ...
Q58632       159 KTEEHAKVAYEAWVGGvDLVKDDEnLTSQEFNKFEDRIYKTLEMRDKAEEETGERKAYMPNITAP-YREMIRRAEIAEDa 237 Methanocaldococ...
Q8THG2       157 TSEMHAEVAYNAFAGGcDLVKDDEnLTDQKFNGFEKRAELTLKIAEKAEAETGERKMYLCNITAPtCEEMIRRLHVLKDl 236 Methanosarcina ...
Q41407       165 QPKPFRAASYALWQGG-AYTTADV-QANQAPTQASEGIPEVVKAMRSCVQGTDVAKRHSGGNYTDePKEMDARGKYVLSq 242 Symbiodinium sp.
O84917       174 RPEPFAQAAYQFWLGG-DFIKNDEpQGNQVFAPVKKVIPLVYDAMKRAQDETGEAKLFSMNITADdYHEMCARADFALEv 252 Thiomonas inter...
ZP_01451219  181 RPEPFAKACLDFWLGG-DFIKNDEpQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADyHGECVARGEYILSe 259 Mariprofundus f...
Q31IK3       172 RPEPFADAAYQFWLGG-DFIKNDEpQGNQTFCPMKKVIPLVADAMKRAQDETGETKLFSANITADdHHEMCYRADYILEt 250 Thiomicrospira ...
YP_003239796 156 SPREQAEVVYEALVGGlDLVKDDEnLTSQPFSPFEERVKRSLEACARAEAEAGEKKVYLPNVTAE-TEEMIRRAELVKRe 234 Ammonifex degen...
Feature 1                                                ##                                #     
4RUB_A       261 g-------vPIVMHDyltgGFTANTSLAHYCRdngLLLHIHRAMHAVIDRq-kNHGIHFRVLAKALRMSGGDHIHSGTVv 332 common tobacco
1RUS_B       275 fge--nashVALLVDgyvaGAAAITTARRRFPd--NFLHYHRAGHGAVTSpqsKRGYTAFVHCKMARLQGASGIHTGTMg 350 Rhodospirillum ...
9RUB_A       251 fge--nashVALLVDgyvaGAAAITTARRRFPd--NFLHYHRAGHGAVTSpqsKRGYTAFVHCKMARLQGASGIHTGTMg 326 Rhodospirillum ...
Q58632       238 g-------sEYVMIDvvvcGFSAVQSFREEDFk--FIIHAHRAMHAAMTRs-rDFGISMLALAKIYRLLGVDQLHIGTVv 307 Methanocaldococ...
Q8THG2       237 g-------aSYAMIDivptGWTALQTLREAAAdegLALHAHRCMHSAFTRn-pRHGVSMLLVAKLCRLIGLDQLHIGTVv 308 Methanosarcina ...
Q41407       243 fgp--fsgnCVSLVA----GYAAGGSARHTFPr--QFVHYHRAGQASTSSpqtQRGYSAFVHTKISQVISTTSIHADTMs 314 Symbiodinium sp.
O84917       253 fgp--dadkLAFLVDgyvgGPGMVTTARRQYPn--QYLHYHRAGHGAITSpssKRGYTAFVLAKMSRLQGASGIHVGTMg 328 Thiomonas inter...
ZP_01451219  260 fakygnekhVAFLIDgfvtGPAGVTTARRAFPd--TFLHFHRAGHGAVTSyksPMGMDPLCYMKLARLQGASGIHTGTMg 337 Mariprofundus f...
Q31IK3       251 fga--dapqVAFLVDgyvgGPGMITTARRNYPs--QYLHYHRAGHGAITSpsaKRGYTAFVLAKISRLQGASGIHVGTMg 326 Thiomicrospira ...
YP_003239796 235 g-------gRYVMVDivtaGFSGLLSLRKANLg--LIIHAHRAMYASFARn-rRHGISMLVLAKLARLAGVDQLHIGTVv 304 Ammonifex degen...
Feature 1          ##                                           ###                      ##      
4RUB_A       333 -GKLEGerdITLGFVDLLRddfveqdrsrgiyftqdwvslPGVLPVASGGIHVWHMPALTEIFG-DDSVLQFGGGTLGHP 410 common tobacco
1RUS_B       351 fGKMEGe-sSDRAIAYMLTqdeaqgpf-----yrqswggmKACTPIISGGMNALRMPGFFENLGnANVILTAGGGAFGHI 424 Rhodospirillum ...
9RUB_A       327 fGKMEGe-sSDRAIAYMLTqdeaqgpf-----yrqswggmKACTPIISGGMNALRMPGFFENLGnANVILTAGGGAFGHI 400 Rhodospirillum ...
Q58632       308 -GKMEGgekEVKAIRDEIVydkveadnen-kffnqdwfdiKPVFPVSSGGVHPRLVPKIVEILG-RDLIIQAGGGVHGHP 384 Methanocaldococ...
Q8THG2       309 -GKMHGdkdEVLSIRDECVldtvpadpeq-hvlaqdwgglKPMFPVASGGLAPTMIPDLYSIFG-KEVIMQFGGGIHAHP 385 Methanosarcina ...
Q41407       315 fGKTQGd-sPDKSIAVMLQddaadarl-----cnqewegmRQNAPIISGSMNALRLPAFFETLGnSNVILTADSGSFGHK 388 Symbiodinium sp.
O84917       329 yGKMEGe-gDDRNIAYMIErdecqgpv-----yfqkwygmKPTTPIISGGMNALRLPGFFENLGhGNVINTAGGGSYGHI 402 Thiomonas inter...
ZP_01451219  338 yGKMEGh-gKETVLAYMLErdecmghy-----fnqkwygmKPTAPIISGGMNALRLPGFFENLGhGNVINTCGGGSFGHI 411 Mariprofundus f...
Q31IK3       327 yGKMEGd-aSDKNIAYMIErdecqgpa-----fyqkwngmKPTTPIISGGMNALRLPGFFENLGhGNVINTSGGGSYGHI 400 Thiomicrospira ...
YP_003239796 305 -GKMEGdkeDVLRCHAALGnaspvsgdl---lrpqdwgeiKPVLSVASGGLHPGHIPDLISIFG-VDCVLQFGGGVHGHP 379 Ammonifex degen...
Feature 1                                                            
4RUB_A       411 WGNAPGAVANRVALEACVKarnegrdlaqegneiIREACKWSPELAAACEVW 462 common tobacco
1RUS_B       425 DGPVAGARSLRQAWQAWRDgv------------pVLDYAREHKELARAFESF 464 Rhodospirillum rubrum
9RUB_A       401 DGPVAGARSLRQAWQAWRDgv------------pVLDYAREHKELARAFESF 440 Rhodospirillum rubrum
Q58632       385 DGTRAGAKAMRAAIEAIIEgk------------sLEEKAEEVAELKKALEYW 424 Methanocaldococcus jannaschii
Q8THG2       386 MGTAAGAAACRQALEASLEgi------------sLQDYAKDHKELEAALGKW 425 Methanosarcina acetivorans
Q41407       389 DGPASGAIACRQVEEAWKAwrsgqyg-nvslsdgVVEFAKTHEEIKGAFLTF 439 Symbiodinium sp.
O84917       403 DSPAAGAKSLRQAYECWKAga------------dPIEYAKEHKEFARAFESF 442 Thiomonas intermedia
ZP_01451219  412 DSPAAGGKSLDQAYDCWKSgt------------dPIEYAKTHGEFARAFESF 451 Mariprofundus ferrooxydans PV-1
Q31IK3       401 DSPAAGATSLRQSYECWKSga------------dPIEFAKDHKEFARAFESF 440 Thiomicrospira crunogena XCL-2
YP_003239796 380 RGTRAGASAVRAAVEAATSgq------------sFQEVARREKTLEEAIMHW 419 Ammonifex degensii KC4

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