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(-) Description

Title :  CRYSTAL STRUCTURE OF RBCX IN COMPLEX WITH SUBSTRATE
 
Authors :  S. Saschenbrecker, A. Bracher, K. Vasudeva Rao, B. Vasudeva Rao, F. U M. Hayer-Hartl
Date :  03 Apr 07  (Deposition) - 10 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B,C,D,E,F,R
Biol. Unit 1:  A,B,R  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Helix Bundle, Protein Complex Assembly, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Saschenbrecker, A. Bracher, K. V. Rao, B. V. Rao, F. U. Hartl, M. Hayer-Hartl
Structure And Function Of Rbcx, An Assembly Chaperone For Hexadecameric Rubisco.
Cell(Cambridge, Mass. ) V. 129 1189 2007
PubMed-ID: 17574029  |  Reference-DOI: 10.1016/J.CELL.2007.04.025

(-) Compounds

Molecule 1 - ORF134
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET11A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneRBCX
    Organism ScientificSYNECHOCOCCUS SP.
    Organism Taxid32049
    StrainPCC 7002
 
Molecule 2 - RBCL
    ChainsR
    EngineeredYES
    FragmentRESIDUES 459-465
    Other DetailsSYNTHETIC PEPTIDE WITH THE SEQUENCE BASED ON RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN (RBCL) FROM SYNECHOCOCCUS SP. PCC 7002, UNP ENTRY Q44176, RBL_SYNP2, RESIDUES 459-465
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit ABCDEFR
Biological Unit 1 (1x)AB    R
Biological Unit 2 (1x)  CD   
Biological Unit 3 (1x)    EF 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2PEM)

(-) Sites  (0, 0)

(no "Site" information available for 2PEM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PEM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PEM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PEM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PEM)

(-) Exons   (0, 0)

(no "Exon" information available for 2PEM)

(-) 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:110
 aligned with Q44177_SYNP2 | Q44177 from UniProtKB/TrEMBL  Length:134

    Alignment length:110
                                    11        21        31        41        51        61        71        81        91       101       111
         Q44177_SYNP2     2 EFKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMMLENKELVLRILTVRENLAEGVLEFLPEMVLSQIKQSNGNHRRSLLERLTQ 111
               SCOP domains d2pema1 A:2-111 RuBisCo chaperone RbcX                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2pem A   2 EFKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMMLENKELVLRILTVRENLAEGVLEFLPEMVLSQIKQSNGNHRRSLLERLTQ 111
                                    11        21        31        41        51        61        71        81        91       101       111

Chain B from PDB  Type:PROTEIN  Length:111
 aligned with Q44177_SYNP2 | Q44177 from UniProtKB/TrEMBL  Length:134

    Alignment length:111
                                    10        20        30        40        50        60        70        80        90       100       110 
         Q44177_SYNP2     1 MEFKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMMLENKELVLRILTVRENLAEGVLEFLPEMVLSQIKQSNGNHRRSLLERLTQ 111
               SCOP domains -d2pemb1 B:2-111 RuBisCo chaperone RbcX                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2pem B   1 MEFKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMMLENKELVLRILTVRENLAEGVLEFLPEMVLSQIKQSNGNHRRSLLERLTQ 111
                                    10        20        30        40        50        60        70        80        90       100       110 

Chain C from PDB  Type:PROTEIN  Length:110
 aligned with Q44177_SYNP2 | Q44177 from UniProtKB/TrEMBL  Length:134

    Alignment length:110
                                    10        20        30        40        50        60        70        80        90       100       110
         Q44177_SYNP2     1 MEFKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMMLENKELVLRILTVRENLAEGVLEFLPEMVLSQIKQSNGNHRRSLLERLT 110
               SCOP domains -d2pemc1 C:2-110 RuBisCo chaperone RbcX                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2pem C   1 MEFKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMMLENKELVLRILTVRENLAEGVLEFLPEMVLSQIKQSNGNHRRSLLERLT 110
                                    10        20        30        40        50        60        70        80        90       100       110

Chain D from PDB  Type:PROTEIN  Length:108
 aligned with Q44177_SYNP2 | Q44177 from UniProtKB/TrEMBL  Length:134

    Alignment length:108
                                    11        21        31        41        51        61        71        81        91       101        
         Q44177_SYNP2     2 EFKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMMLENKELVLRILTVRENLAEGVLEFLPEMVLSQIKQSNGNHRRSLLERL 109
               SCOP domains d2pemd1 D:2-109 RuBisCo chaperone RbcX                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2pem D   2 EFKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMMLENKELVLRILTVRENLAEGVLEFLPEMVLSQIKQSNGNHRRSLLERL 109
                                    11        21        31        41        51        61        71        81        91       101        

Chain E from PDB  Type:PROTEIN  Length:112
 aligned with Q44177_SYNP2 | Q44177 from UniProtKB/TrEMBL  Length:134

    Alignment length:112
                                    11        21        31        41        51        61        71        81        91       101       111  
         Q44177_SYNP2     2 EFKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMMLENKELVLRILTVRENLAEGVLEFLPEMVLSQIKQSNGNHRRSLLERLTQVD 113
               SCOP domains d2peme1 E:2-111 RuBisCo chaperone RbcX                                                                        -- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2pem E   2 EFKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMMLENKELVLRILTVRENLAEGVLEFLPEMVLSQIKQSNGNHRRSLLERLTQVD 113
                                    11        21        31        41        51        61        71        81        91       101       111  

Chain F from PDB  Type:PROTEIN  Length:110
 aligned with Q44177_SYNP2 | Q44177 from UniProtKB/TrEMBL  Length:134

    Alignment length:110
                                    12        22        32        42        52        62        72        82        92       102       112
         Q44177_SYNP2     3 FKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMMLENKELVLRILTVRENLAEGVLEFLPEMVLSQIKQSNGNHRRSLLERLTQV 112
               SCOP domains d2pemf1 F:3-111 RuBisCo chaperone RbcX                                                                       - SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) RcbX-2pemF01 F:3-111                                                                                         - Pfam domains (1)
           Pfam domains (2) RcbX-2pemF02 F:3-111                                                                                         - Pfam domains (2)
           Pfam domains (3) RcbX-2pemF03 F:3-111                                                                                         - Pfam domains (3)
           Pfam domains (4) RcbX-2pemF04 F:3-111                                                                                         - Pfam domains (4)
           Pfam domains (5) RcbX-2pemF05 F:3-111                                                                                         - Pfam domains (5)
           Pfam domains (6) RcbX-2pemF06 F:3-111                                                                                         - Pfam domains (6)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2pem F   3 FKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMMLENKELVLRILTVRENLAEGVLEFLPEMVLSQIKQSNGNHRRSLLERLTQV 112
                                    12        22        32        42        52        62        72        82        92       102       112

Chain R from PDB  Type:PROTEIN  Length:7
 aligned with RBL_SYNP2 | Q44176 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:7
            RBL_SYNP2   459 EIKFEFD 465
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 2pem R 459 EIKFEFD 465

   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  (1, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PEM)

(-) Pfam Domains  (1, 6)

Asymmetric Unit

(-) Gene Ontology  (11, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q44177_SYNP2 | Q44177)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

Chain R   (RBL_SYNP2 | Q44176)
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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q44177_SYNP2 | Q441772pei 2pej 2pek 2pen 2peq 2z44 2z45 2z46

(-) Related Entries Specified in the PDB File

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2pek CRYSTAL STRUCTURE OF RBCX MUTANT Q29A
2pen CRYSTAL STRUCTURE OF RBCX, CRYSTAL FORM I
2peo CRYSTAL STRUCTURE OF RBCX FROM ANABAENA CA
2peq CRYSTAL STRUCTURE OF RBCX, CRYSTAL FORM II