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(-) Description

Title :  SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE AND CALCIUM.
 
Authors :  S. Karkehabadi, T. C. Taylor, I. Andersson
Date :  09 Oct 03  (Deposition) - 14 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,C,E,G,I,J,K,L
Biol. Unit 1:  A,C,E,G,I,J,K,L  (2x)
Keywords :  Lyase, Carbon-Carbon, Oxidoreductase, Photosynthesis, Carbon-Dioxide Fixation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Karehabadi, T. C. Taylor, I. Andersson
Calcium Supports Loop Closure But Not Catalysis In Rubisco
J. Mol. Biol. V. 334 65 2003
PubMed-ID: 14596800  |  Reference-DOI: 10.1016/J.JMB.2003.09.025

(-) Compounds

Molecule 1 - RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
    Chains: A, C, E, G
    EC Number: 4.1.1.39
    Organ: LEAF
    Organism Common: SPINACH
    Organism Scientific: SPINACIA OLERACEA
    Organism Taxid: 3562
    Synonym: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE, RUBISCO LARGE SUBUNIT
 
Molecule 2 - RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
    Chains: I, J, K, L
    EC Number: 4.1.1.39
    Organ: LEAF
    Organism Common: SPINACH
    Organism Scientific: SPINACIA OLERACEA
    Organism Taxid: 3562
    Other Details: THIS IS THE SECOND STRUCTURE OF THIS COMPLEX THAT IS BEING SUBMITTED. THE PREVOUS STRUCTURE, PDB ID CODE 1UPM, WAS OBTAINED FROM A CRYSTAL OF RUBISCO-CA COOCRYSTALLIZED WITH 2-CABP WHERAS THIS STRUCTURE IS FROM A RUBISCO-CA/3PGA CRYSTAL WHICH WAS SOAKED WITH 2-CABP
    Synonym: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE, RUBISCO SMALL SUBUNIT

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ACEGIJKL
Biological Unit 1 (2x): ACEGIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CAP4Ligand/Ion2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
3KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CAP8Ligand/Ion2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
3KCX8Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:175 , LYS A:177 , KCX A:201 , ASP A:203 , GLU A:204 , CAP A:477BINDING SITE FOR RESIDUE CA A 476
2AC2SOFTWARELYS C:175 , LYS C:177 , KCX C:201 , ASP C:203 , GLU C:204 , CAP C:477BINDING SITE FOR RESIDUE CA C 476
3AC3SOFTWARELYS E:177 , KCX E:201 , ASP E:203 , GLU E:204 , CAP E:477BINDING SITE FOR RESIDUE CA E 476
4AC4SOFTWARELYS G:177 , KCX G:201 , ASP G:203 , GLU G:204 , CAP G:477BINDING SITE FOR RESIDUE CA G 476
5AC5SOFTWARETHR A:173 , LYS A:175 , LYS A:177 , KCX A:201 , GLU A:204 , HIS A:294 , ARG A:295 , HIS A:327 , LYS A:334 , LEU A:335 , SER A:379 , GLY A:380 , GLY A:381 , GLY A:403 , GLY A:404 , CA A:476 , HOH A:2070 , HOH A:2110 , HOH A:2111 , HOH A:2112 , GLU E:60 , THR E:65 , TRP E:66 , ASN E:123 , HOH E:2016BINDING SITE FOR RESIDUE CAP A 477
6AC6SOFTWAREGLU C:60 , THR C:65 , TRP C:66 , ASN C:123 , THR C:173 , LYS C:175 , LYS C:177 , KCX C:201 , HIS C:294 , ARG C:295 , HIS C:327 , LYS C:334 , LEU C:335 , SER C:379 , GLY C:380 , GLY C:381 , PHE C:402 , GLY C:403 , GLY C:404 , CA C:476 , HOH C:2082 , HOH C:2083 , HOH C:2105 , HOH C:2108BINDING SITE FOR RESIDUE CAP C 477
7AC7SOFTWAREGLU A:60 , THR A:65 , TRP A:66 , ASN A:123 , THR E:173 , LYS E:175 , LYS E:177 , KCX E:201 , HIS E:294 , ARG E:295 , HIS E:327 , LYS E:334 , LEU E:335 , SER E:379 , GLY E:380 , GLY E:381 , GLY E:403 , GLY E:404 , CA E:476 , HOH E:2080 , HOH E:2081 , HOH E:2129 , HOH E:2130 , HOH E:2131 , HOH E:2132BINDING SITE FOR RESIDUE CAP E 477
8AC8SOFTWAREGLU G:60 , THR G:65 , TRP G:66 , ASN G:123 , THR G:173 , LYS G:175 , LYS G:177 , KCX G:201 , HIS G:294 , ARG G:295 , HIS G:327 , LYS G:334 , LEU G:335 , SER G:379 , GLY G:380 , GLY G:381 , GLY G:403 , GLY G:404 , CA G:476 , HOH G:2088 , HOH G:2104 , HOH G:2132 , HOH G:2133BINDING SITE FOR RESIDUE CAP G 477

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:247 -E:247

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys C:175 -Pro C:176

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UPP)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUBISCO_LARGEPS00157 Ribulose bisphosphate carboxylase large chain active site.RBL_SPIOL196-204
 
 
 		  4A:196-204
C:196-204
E:196-204
G:196-204
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUBISCO_LARGEPS00157 Ribulose bisphosphate carboxylase large chain active site.RBL_SPIOL196-204
 
 
 		  8A:196-204
C:196-204
E:196-204
G:196-204

(-) Exons   (0, 0)

(no "Exon" information available for 1UPP)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:467
 aligned with RBL_SPIOL | P00875 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:467
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       
            RBL_SPIOL     9 ASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSRGIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV 475
               SCOP domains d1uppa1 A:9-147 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                            d1uppa2 A:148-475 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------1uppA01 A:22-148  [code=3.30.70.150, no name defined]                                                                          1uppA02 A:149-462 Rubisco                                                                                                                                                                                                                                                                                                 ------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhh..........eeeeeeeee....hhhhhhhhhhhhh.......hhhhhhhhhhhhh.eeeeeee.......eeeeeeehhhhh...hhhhhhhhhh.hhhhh..eeeeeeeeee.hhhhhh.......hhhhhhhhhh.....eee.........hhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhh....eehhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhh.ee...hhhh....ee.......eeeee...hhhhhhhhhhhhh...eee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RUBISCO_L------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1upp A   9 ASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTkDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSRGIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV 475
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198  |    208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       
                                                                                                                                                                                                                          201-KCX                                                                                                                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:467
 aligned with RBL_SPIOL | P00875 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:467
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       
            RBL_SPIOL     9 ASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSRGIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV 475
               SCOP domains d1uppc1 C:9-147 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                            d1uppc2 C:148-475 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------1uppC01 C:22-148  [code=3.30.70.150, no name defined]                                                                          1uppC02 C:149-462 Rubisco                                                                                                                                                                                                                                                                                                 ------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhh..........eeeeeeeee....hhhhhhhhhhhhh.......hhhhhhhhhhhhh.eeeeeee.......eeeeeeehhhhh...hhhhhhhhhh.hhhhh..eeeeeeeeee.hhhhhh.......hhhhhhhhhh.....eee.........hhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhh....eehhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhh.ee...hhhh....ee.......eeeee...hhhhhhhhhhhhh...eee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RUBISCO_L------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1upp C   9 ASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTkDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSRGIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV 475
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198  |    208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       
                                                                                                                                                                                                                          201-KCX                                                                                                                                                                                                                                                                              


Chain E from PDB  Type:PROTEIN  Length:467
 aligned with RBL_SPIOL | P00875 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:467
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       
            RBL_SPIOL     9 ASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSRGIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV 475
               SCOP domains d1uppe1 E:9-147 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                            d1uppe2 E:148-475 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------1uppE01 E:22-148  [code=3.30.70.150, no name defined]                                                                          1uppE02 E:149-462 Rubisco                                                                                                                                                                                                                                                                                                 ------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhh..........eeeeeeeee....hhhhhhhhhhhhh.......hhhhhhhhhhhhh.eeeeeee.......eeeeeeehhhhh...hhhhhhhhhh.hhhhh..eeeeeeeeee.hhhhhh.......hhhhhhhhhh.....eee.........hhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhh...eeeee..hhhhhhh....eehhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhh.ee...hhhh....ee.......eeee....hhhhhhhhhhhhh...eee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RUBISCO_L------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1upp E   9 ASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTkDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSRGIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV 475
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198  |    208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       
                                                                                                                                                                                                                          201-KCX                                                                                                                                                                                                                                                                              


Chain G from PDB  Type:PROTEIN  Length:467
 aligned with RBL_SPIOL | P00875 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:467
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       
            RBL_SPIOL     9 ASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSRGIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV 475
               SCOP domains d1uppg1 G:9-147 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                            d1uppg2 G:148-475 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------1uppG01 G:22-148  [code=3.30.70.150, no name defined]                                                                          1uppG02 G:149-462 Rubisco                                                                                                                                                                                                                                                                                                 ------------- CATH domains
           Pfam domains (1) ------------RuBisCO_large_N-1uppG05 G:21-146                                                                                              -------RuBisCO_large-1uppG01 G:154-462                                                                                                                                                                                                                                                                                      ------------- Pfam domains (1)
           Pfam domains (2) ------------RuBisCO_large_N-1uppG06 G:21-146                                                                                              -------RuBisCO_large-1uppG02 G:154-462                                                                                                                                                                                                                                                                                      ------------- Pfam domains (2)
           Pfam domains (3) ------------RuBisCO_large_N-1uppG07 G:21-146                                                                                              -------RuBisCO_large-1uppG03 G:154-462                                                                                                                                                                                                                                                                                      ------------- Pfam domains (3)
           Pfam domains (4) ------------RuBisCO_large_N-1uppG08 G:21-146                                                                                              -------RuBisCO_large-1uppG04 G:154-462                                                                                                                                                                                                                                                                                      ------------- Pfam domains (4)
         Sec.struct. author ...........hhhhhh..........eeeeeeeee....hhhhhhhhhhhhh.......hhhhhhhhhhhh..eeeeeee.......eeeeeeehhhhh...hhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhh.......hhhhhhhhhh.....eee.........hhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhh.eeee...hhhhhhh....eehhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhh.ee...hhhh....ee.......eeeee...hhhhhhhhhhhhh...eee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RUBISCO_L------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1upp G   9 ASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTkDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSRGIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV 475
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198  |    208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       
                                                                                                                                                                                                                          201-KCX                                                                                                                                                                                                                                                                              


Chain I from PDB  Type:PROTEIN  Length:123
 aligned with RBS2_SPIOL | Q43832 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:123
                                    67        77        87        97       107       117       127       137       147       157       167       177   
           RBS2_SPIOL    58 MKVWPTQNMKRYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPGYYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNRQVQCVSFIAYKPAGY 180
               SCOP domains d1uppi_ I: Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                  SCOP domains
               CATH domains 1uppI00 I:1-123  [code=3.30.190.10, no name defined]                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhh..eeeeeee......................eee........hhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1upp I   1 MQVWPILNLKKYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPGYYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNREVQCISFIAYKPAGY 123
                                    10        20        30        40        50        60        70        80        90       100       110       120   


Chain J from PDB  Type:PROTEIN  Length:123
 aligned with RBS2_SPIOL | Q43832 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:123
                                    67        77        87        97       107       117       127       137       147       157       167       177   
           RBS2_SPIOL    58 MKVWPTQNMKRYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPGYYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNRQVQCVSFIAYKPAGY 180
               SCOP domains d1uppj_ J: Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                  SCOP domains
               CATH domains 1uppJ00 J:1-123  [code=3.30.190.10, no name defined]                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhh..eeeeeee......................ee.........hhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1upp J   1 MQVWPILNLKKYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPGYYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNREVQCISFIAYKPAGY 123
                                    10        20        30        40        50        60        70        80        90       100       110       120   


Chain K from PDB  Type:PROTEIN  Length:123
 aligned with RBS2_SPIOL | Q43832 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:123
                                    67        77        87        97       107       117       127       137       147       157       167       177   
           RBS2_SPIOL    58 MKVWPTQNMKRYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPGYYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNRQVQCVSFIAYKPAGY 180
               SCOP domains d1uppk_ K: Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                  SCOP domains
               CATH domains 1uppK00 K:1-123  [code=3.30.190.10, no name defined]                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhh..eeeeeee......................ee.........hhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1upp K   1 MQVWPILNLKKYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPGYYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNREVQCISFIAYKPAGY 123
                                    10        20        30        40        50        60        70        80        90       100       110       120   


Chain L from PDB  Type:PROTEIN  Length:123
 aligned with RBS2_SPIOL | Q43832 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:123
                                    67        77        87        97       107       117       127       137       147       157       167       177   
           RBS2_SPIOL    58 MKVWPTQNMKRYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPGYYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNRQVQCVSFIAYKPAGY 180
               SCOP domains d1uppl_ L: Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                  SCOP domains
               CATH domains 1uppL00 L:1-123  [code=3.30.190.10, no name defined]                                                                        CATH domains
           Pfam domains (1) ----------RuBisCO_small-1uppL01 L:11-121                                                                                 -- Pfam domains (1)
           Pfam domains (2) ----------RuBisCO_small-1uppL02 L:11-121                                                                                 -- Pfam domains (2)
           Pfam domains (3) ----------RuBisCO_small-1uppL03 L:11-121                                                                                 -- Pfam domains (3)
           Pfam domains (4) ----------RuBisCO_small-1uppL04 L:11-121                                                                                 -- Pfam domains (4)
         Sec.struct. author .....................hhhhhhhhhhhhhhh..eeeeeee......................eee........hhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1upp L   1 MQVWPILNLKKYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPGYYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNREVQCISFIAYKPAGY 123
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 12)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 12)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (3, 12)

Asymmetric Unit
(-)
Clan: no clan defined [family: RuBisCO_large] (36)
(-)
Clan: no clan defined [family: RuBisCO_large_N] (27)
(-)
Clan: no clan defined [family: RuBisCO_small] (23)

(-) Gene Ontology  (13, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G   (RBL_SPIOL | P00875)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016984    ribulose-bisphosphate carboxylase activity    Catalysis of the reaction: D-ribulose 1,5-bisphosphate + CO2 + H2O = 2 3-phospho-D-glycerate.
biological process
    GO:0015977    carbon fixation    A metabolic process in which carbon (usually derived from carbon dioxide) is incorporated into organic compounds (usually carbohydrates).
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0009853    photorespiration    A light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved. The substrate is glycolate formed in large quantities in chloroplasts from 2-phosphoglycolate generated from ribulose 1,5-bisphosphate by the action of ribulose-bisphosphate carboxylase; the glycolate enters the peroxisomes where it is converted by glycolate oxidase to glyoxylate which undergoes transamination to glycine. This then passes into the mitochondria where it is decarboxylated forming one molecule of serine for every two molecules of glycine. This pathway also exists in photosynthetic bacteria.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
    GO:0019253    reductive pentose-phosphate cycle    The fixation of carbon dioxide (CO2) as glucose in the chloroplasts of C3 plants; uses ATP and NADPH formed in the light reactions of photosynthesis; carbon dioxide reacts with ribulose 1,5-bisphosphate (catalyzed by the function of ribulose-bisphosphate carboxylase) to yield two molecules of 3-phosphoglycerate; these are then phosphorylated by ATP to 1,3-bisphosphateglyceraldehyde which, in turn, is then reduced by NADPH to glyceraldehyde 3-phosphate. The glyceraldehyde 3-phosphate is converted to fructose 5-phosphate and ribulose 5-phosphate by aldolase and other enzymes; the ribulose 5-phosphate is phosphorylated by ATP to ribulose 1,5-bisphosphate.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

Chain I,J,K,L   (RBS2_SPIOL | Q43832)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016984    ribulose-bisphosphate carboxylase activity    Catalysis of the reaction: D-ribulose 1,5-bisphosphate + CO2 + H2O = 2 3-phospho-D-glycerate.
biological process
    GO:0015977    carbon fixation    A metabolic process in which carbon (usually derived from carbon dioxide) is incorporated into organic compounds (usually carbohydrates).
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0009853    photorespiration    A light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved. The substrate is glycolate formed in large quantities in chloroplasts from 2-phosphoglycolate generated from ribulose 1,5-bisphosphate by the action of ribulose-bisphosphate carboxylase; the glycolate enters the peroxisomes where it is converted by glycolate oxidase to glyoxylate which undergoes transamination to glycine. This then passes into the mitochondria where it is decarboxylated forming one molecule of serine for every two molecules of glycine. This pathway also exists in photosynthetic bacteria.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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  1upp
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  RBL_SPIOL | P00875
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  RBS2_SPIOL | Q43832
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  4.1.1.39
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RBL_SPIOL | P00875: 1aa1 1aus 1ir1 1rbo 1rco 1rcx 1rxo 1upm 8ruc
        RBS2_SPIOL | Q43832: 1aa1 1aus 1ir1 1upm 1uzd

(-) Related Entries Specified in the PDB File

1aa1 ACTIVATED SPINACH RUBISCO IN COMPLEX WITH THE PRODUCT 3-PHOSPHOGLYCERATE
1aus ACTIVATED UNLIGANDED SPINACH RUBISCO
1ir1 CRYSTAL STRUCTURE OF SPINACH RIBULOSE-1,5- BISPHOSPHATECARBOXYLASE/OXYGENASE (RUBISCO) COMPLEXED WITH CO2, MG2+AND 2- CARBOXYARABINITOL-1,5-BISPHOSPHATE
1rbo SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
1rco SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR D-XYLULOSE-2,2-DIOL-1,5- BISPHOSPHATE
1rcx NON-ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE
1rxo ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE AND CALCIUM
1upm ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+
8ruc ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2- CARBOXYARABINITOL BISPHOSPHATE