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(-) Description

Title :  CRYSTAL STRUCTURE OF OCTAMERIC RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (RUBISCO) FROM PYROCOCCUS HORIKOSHII OT3 (FORM-1 CRYSTAL)
 
Authors :  E. Mizohata, C. Mishima, R. Akasaka, H. Uda, T. Terada, M. Shirouzu, S. Y Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  27 Jun 05  (Deposition) - 27 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,E
Biol. Unit 1:  A,E  (4x)
Biol. Unit 2:  A,E  (1x)
Keywords :  Lyase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Mizohata, C. Mishima, R. Akasaka, H. Uda, T. Terada, M. Shirouzu, S. Yokoyama
Crystal Structure Of Octameric Ribulose-1, 5-Bisphosphate Carboxylase/Oxygenase (Rubisco) From Pyrococcus Horikoshii Ot3 (Form-1 Crystal)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBULOSE BISPHOSPHATE CARBOXYLASE
    Chains: A, E
    EC Number: 4.1.1.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, RUBISCO

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AE
Biological Unit 1 (4x): AE
Biological Unit 2 (1x): AE

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2CWX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:160 -Pro A:161
2Lys E:160 -Pro E:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CWX)

(-) 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:414
 aligned with RBL_PYRHO | O58677 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:417
                                    17        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       
            RBL_PYRHO     8 VEWYLDFVDLNYEPGRDELIVEYYFEPNGVSPEEAAGRIASESSIGTWTTLWKLPEMAKRSMAKVFYLEKHGEGYIAKIAYPLTLFEEGSLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVKDRPLTATVPKPKMGWSVEEYAEIAYELWSGGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGPVNIMEKRAEMVANEGGQYVMIDIVVAGWSALQYMREVTEDLGLAIHAHRAMHAAFTRNPRHGITMLALAKAARMIGVDQIHTGTAVGKMAGNYEEIKRINDFLLSKWEHIRPVFPVASGGLHPGLMPELIRLFGKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREVGLSKA 424
               SCOP domains d2cwxa2 A:8-133 Ribulose 1,5-bisphosphate carbo   xylase-oxygenase                                                            d2cwxa1 A:134-424 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2cwxA01 A:8-133  [code=3.30.70.150, no name def   ined]                                                                       2cwxA02 A:134-419 Rubisco                                                                                                                                                                                                                                                                     ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...........eeeeeeeeee...hhhhhhhhhhhhh....---....hhhhhhh..eeeeeeee..eeeeeeeee.hhh...hhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhh......hhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhhh..eee...........hhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhh....eehhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhh...eeehhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cwx A   8 VEWYLDFVDLNYEPGRDELIVEYYFEPNGVSPEEAAGRIASESSIGT---LWKLPEMAKRSMAKVFYLEKHGEGYIAKIAYPLTLFEEGSLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVKDRPLTATVPKPKMGWSVEEYAEIAYELWSGGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGPVNIMEKRAEMVANEGGQYVMIDIVVAGWSALQYMREVTEDLGLAIHAHRAMHAAFTRNPRHGITMLALAKAARMIGVDQIHTGTAVGKMAGNYEEIKRINDFLLSKWEHIRPVFPVASGGLHPGLMPELIRLFGKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREVGLSKA 424
                                    17        27        37        47      |  -|       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       
                                                                         54  58                                                                                                                                                                                                                                                                                                                                                                              


Chain E from PDB  Type:PROTEIN  Length:408
 aligned with RBL_PYRHO | O58677 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:408
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409        
            RBL_PYRHO    10 WYLDFVDLNYEPGRDELIVEYYFEPNGVSPEEAAGRIASESSIGTWTTLWKLPEMAKRSMAKVFYLEKHGEGYIAKIAYPLTLFEEGSLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVKDRPLTATVPKPKMGWSVEEYAEIAYELWSGGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGPVNIMEKRAEMVANEGGQYVMIDIVVAGWSALQYMREVTEDLGLAIHAHRAMHAAFTRNPRHGITMLALAKAARMIGVDQIHTGTAVGKMAGNYEEIKRINDFLLSKWEHIRPVFPVASGGLHPGLMPELIRLFGKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLR 417
               SCOP domains d2cwxe2 E:10-133 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                            d2cwxe1 E:134-417 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                            SCOP domains
               CATH domains 2cwxE01 E:10-133  [code=3.30.70.150, no name defined]                                                                       2cwxE02 E:134-417 Rubisco                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh..........eeeeeeeee...hhhhhhhhhhhhh..............hhhhh.eeeeeeee..eeeeeeeehhhhh...hhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhh......hhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhhh..eee...........hhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhh....eehhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhh...eeehhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cwx E  10 WYLDFVDLNYEPGRDELIVEYYFEPNGVSPEEAAGRIASESSIGTWTTLWKLPEMAKRSMAKVFYLEKHGEGYIAKIAYPLTLFEEGSLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVKDRPLTATVPKPKMGWSVEEYAEIAYELWSGGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGPVNIMEKRAEMVANEGGQYVMIDIVVAGWSALQYMREVTEDLGLAIHAHRAMHAAFTRNPRHGITMLALAKAARMIGVDQIHTGTAVGKMAGNYEEIKRINDFLLSKWEHIRPVFPVASGGLHPGLMPELIRLFGKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLR 417
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409
   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  (2, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CWX)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,E   (RBL_PYRHO | O58677)
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: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:0006196    AMP catabolic process    The chemical reactions and pathways resulting in the breakdown of AMP, adenosine monophosphate.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RBL_PYRHO | O58677: 2cxe 2d69

(-) Related Entries Specified in the PDB File

2cxe FORM-2 CRYSTAL RELATED ID: PHO001000939.2 RELATED DB: TARGETDB