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(-) Description

Title :  CRYSTAL STRUCTURE OF UNACTIVATED TOBACCO RUBISCO WITH BOUND PHOSPHATE IONS
 
Authors :  A. P. Duff, T. J. Andrews, P. M. G. Curmi
Date :  01 Mar 00  (Deposition) - 15 Mar 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  L,S
Biol. Unit 1:  L,S  (8x)
Keywords :  Tim Barrel, Alpha/Beta Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. P. Duff, T. J. Andrews, P. M. G. Curmi
The Transition Between The Open And Closed States Of Rubisc Is Triggered By The Inter-Phosphate Distance Of The Bound Bisphosphate.
J. Mol. Biol. V. 298 903 2000
PubMed-ID: 10801357  |  Reference-DOI: 10.1006/JMBI.2000.3724

(-) Compounds

Molecule 1 - RUBISCO (LARGE SUBUNIT)
    ChainsL
    EC Number4.1.1.39
    OrganLEAF
    Organism CommonCOMMON TOBACCO
    Organism ScientificNICOTIANA TABACUM
    Organism Taxid4097
    VariantWISCONSIN-38
 
Molecule 2 - RUBISCO (SMALL SUBUNIT)
    ChainsS
    EC Number4.1.1.39
    OrganLEAF
    Organism CommonCOMMON TOBACCO
    Organism ScientificNICOTIANA TABACUM
    Organism Taxid4097
    VariantWISCONSIN-38

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit LS
Biological Unit 1 (8x)LS

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 24)
No.NameCountTypeFull Name
1PO424Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP L:66 , GLY L:381 , PHE L:402 , GLY L:403 , GLY L:404 , HOH L:870BINDING SITE FOR RESIDUE PO4 L 641
2AC2SOFTWAREARG L:295 , HIS L:298 , HOH L:714 , HOH L:850BINDING SITE FOR RESIDUE PO4 L 642
3AC3SOFTWAREARG L:134 , LYS L:305 , HIS L:310 , HOH L:811 , HOH L:819BINDING SITE FOR RESIDUE PO4 L 643

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1L:247 -L:247

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_RBL_TOBAC_001 *F394VRBL_TOBAC  ---  ---LF394V
2UniProtVAR_RBL_TOBAC_002 *G405MRBL_TOBAC  ---  ---LG405M
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_RBL_TOBAC_001 *F394VRBL_TOBAC  ---  ---LF394V
2UniProtVAR_RBL_TOBAC_002 *G405MRBL_TOBAC  ---  ---LG405M
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUBISCO_LARGEPS00157 Ribulose bisphosphate carboxylase large chain active site.RBL_TOBAC196-204  1L:196-204
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUBISCO_LARGEPS00157 Ribulose bisphosphate carboxylase large chain active site.RBL_TOBAC196-204  8L:196-204

(-) Exons   (0, 0)

(no "Exon" information available for 1EJ7)

(-) 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 L from PDB  Type:PROTEIN  Length:457
 aligned with RBL_TOBAC | P00876 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:457
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       
            RBL_TOBAC    18 KEYKLTYYTPEYQTKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIERVVGEKDQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFVEQDRSRGIYFTQDWVSLPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVKARNEGRDLAQEGNEIIREACKWSPELAAACEVWKEIVFNFAAVDV 474
               SCOP domains d1ej7l2 L:18-147 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                  d1ej7l1 L:148-474 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----1ej7L01 L:22-148  [code=3.30.70.150, no name defined]                                                                          1ej7L02 L:149-467 Rubisco                                                                                                                                                                                                                                                                                                      ------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..........eeeeeeeee....hhhhhhhhhhhhh.......hhhhhh.hhhhhh.eeeeeee.......eeeeeeehhhhh...hhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhh.......hhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhh....eehhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhh.ee...hhhh....ee.......eeeee...hhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V----------M--------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RUBISCO_L------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ej7 L  18 KDYKLTYYTPEYQTKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIERVVGEKDQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFVEQDRSRGIYFTQDWVSLPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVKARNEGRDLAQEGNEIIREACKWSPELAAACEVWKEIVFNFAAVDV 474
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       

Chain S from PDB  Type:PROTEIN  Length:123
 aligned with RBS_TOBAC | P69249 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:123
                                    67        77        87        97       107       117       127       137       147       157       167       177   
            RBS_TOBAC    58 MQVWPPINKKKYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFETEHGFVYRENNKSPGYYDGRYWTMWKLPMFGCTDATQVLAEVEEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKPEGY 180
               SCOP domains d1ej7s_ S: Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                  SCOP domains
               CATH domains 1ej7S00 S:501-623  [code=3.30.190.10, no name defined]                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhh.eeeeeee......................eee........hhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ej7 S 501 MQVWPPINKKKYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFETEHGFVYRENNKSPGYYDGRYWTMWKLPMFGCTDATQVLAEVEEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKPEGY 623
                                   510       520       530       540       550       560       570       580       590       600       610       620   

   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, 3)

Asymmetric Unit

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EJ7)

(-) Gene Ontology  (14, 24)

Asymmetric Unit(hide GO term definitions)
Chain L   (RBL_TOBAC | P00876)
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 S   (RBS_TOBAC | P69249)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        RBL_TOBAC | P008761rlc 1rld 3rub 4rub
        RBS_TOBAC | P692491rlc 1rld 3rub 4rub

(-) Related Entries Specified in the PDB File

8ruc INITIAL PHASING MODEL