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(-) Description

Title :  D-RIBULOSE-5-PHOSPHATE 3-EPIMERASE FROM SOLANUM TUBEROSUM CHLOROPLASTS
 
Authors :  J. Kopp, G. E. Schulz
Date :  01 Dec 98  (Deposition) - 07 Apr 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  3-Epimerase, Chloroplast, Calvin Cycle, Oxidative Pentose Phosphate Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Kopp, S. Kopriva, K. H. Suss, G. E. Schulz
Structure And Mechanism Of The Amphibolic Enzyme D-Ribulose-5-Phosphate 3-Epimerase From Potato Chloroplasts
J. Mol. Biol. V. 287 761 1999
PubMed-ID: 10191144  |  Reference-DOI: 10.1006/JMBI.1999.2643

(-) Compounds

Molecule 1 - PROTEIN (RIBULOSE-PHOSPHATE 3-EPIMERASE)
    ChainsA, B, C
    EC Number5.1.3.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    OrganelleCHLOROPLAST
    Organism CommonPOTATO
    Organism ScientificSOLANUM TUBEROSUM
    Organism Taxid4113

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (2x)ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:187 , GLY A:207 , SER A:208 , HOH A:232 , HOH A:238BINDING SITE FOR RESIDUE SO4 A 231
2AC2SOFTWAREGLY B:187 , GLY B:207 , SER B:208 , HOH B:235 , HOH B:241BINDING SITE FOR RESIDUE SO4 B 232
3AC3SOFTWAREGLY C:187 , GLY C:207 , SER C:208 , HOH C:236 , HOH C:241BINDING SITE FOR RESIDUE SO4 C 233

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RPX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RPX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBUL_P_3_EPIMER_1PS01085 Ribulose-phosphate 3-epimerase family signature 1.RPE_SOLTU86-100
 
 
  3A:40-54
B:40-54
C:40-54
2RIBUL_P_3_EPIMER_2PS01086 Ribulose-phosphate 3-epimerase family signature 2.RPE_SOLTU190-212
 
 
  3A:144-166
B:144-166
C:144-166
Biological Unit 1 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBUL_P_3_EPIMER_1PS01085 Ribulose-phosphate 3-epimerase family signature 1.RPE_SOLTU86-100
 
 
  6A:40-54
B:40-54
C:40-54
2RIBUL_P_3_EPIMER_2PS01086 Ribulose-phosphate 3-epimerase family signature 2.RPE_SOLTU190-212
 
 
  6A:144-166
B:144-166
C:144-166

(-) Exons   (0, 0)

(no "Exon" information available for 1RPX)

(-) 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:230
 aligned with RPE_SOLTU | Q43843 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:230
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276
            RPE_SOLTU    47 SRVDKFSKSDIIVSPSILSANFSKLGEQVKAIEQAGCDWIHVDVMDGRFVPNITIGPLVVDSLRPITDLPLDVHLMIVEPDQRVPDFIKAGADIVSVHCEQSSTIHLHRTINQIKSLGAKAGVVLNPGTPLTAIEYVLDAVDLVLIMSVNPGFGGQSFIESQVKKISDLRKICAERGLNPWIEVDGGVGPKNAYKVIEAGANALVAGSAVFGAPDYAEAIKGIKTSKRPE 276
               SCOP domains d1rpxa_ A: D-ribulose-5-phosphate 3-epimerase                                                                                                                                                                                          SCOP domains
               CATH domains 1rpxA00 A:1-230 Aldolase class I                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh......eeeeehhh..hhhhhhhhhhhhh....eeeeeee...........hhhhhhhhhh...eeeeeee...hhhhhhhhhh....eeeee........hhhhhhhhhh...eeeeee.....hhhh........eeeee............hhhhhhhhhhhhhhhhh....eeeee.......hhhhhhh...eeee.hhhh....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RIBUL_P_3_EPIME-----------------------------------------------------------------------------------------RIBUL_P_3_EPIMER_2     ---------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rpx A   1 SRVDKFSKSDIIVSPSILSANFSKLGEQVKAIEQAGCDWIHVDVMDGRFVPNITIGPLVVDSLRPITDLPLDVHLMIVEPDQRVPDFIKAGADIVSVHCEQSSTIHLHRTINQIKSLGAKAGVVLNPGTPLTAIEYVLDAVDLVLIMSVNPGFGGQSFIESQVKKISDLRKICAERGLNPWIEVDGGVGPKNAYKVIEAGANALVAGSAVFGAPDYAEAIKGIKTSKRPE 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:230
 aligned with RPE_SOLTU | Q43843 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:230
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276
            RPE_SOLTU    47 SRVDKFSKSDIIVSPSILSANFSKLGEQVKAIEQAGCDWIHVDVMDGRFVPNITIGPLVVDSLRPITDLPLDVHLMIVEPDQRVPDFIKAGADIVSVHCEQSSTIHLHRTINQIKSLGAKAGVVLNPGTPLTAIEYVLDAVDLVLIMSVNPGFGGQSFIESQVKKISDLRKICAERGLNPWIEVDGGVGPKNAYKVIEAGANALVAGSAVFGAPDYAEAIKGIKTSKRPE 276
               SCOP domains d1rpxb_ B: D-ribulose-5-phosphate 3-epimerase                                                                                                                                                                                          SCOP domains
               CATH domains 1rpxB00 B:1-230 Aldolase class I                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh......eeeeehhh..hhhhhhhhhhhhh....eeeeeee...........hhhhhhhhhh...eeeeeee...hhhhhhhhhh....eeeee........hhhhhhhhhh...eeeeee.....hhhh........eeeee............hhhhhhhhhhhhhhhhh....eeeee.......hhhhhhh...eeee.hhhh....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RIBUL_P_3_EPIME-----------------------------------------------------------------------------------------RIBUL_P_3_EPIMER_2     ---------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rpx B   1 SRVDKFSKSDIIVSPSILSANFSKLGEQVKAIEQAGCDWIHVDVMDGRFVPNITIGPLVVDSLRPITDLPLDVHLMIVEPDQRVPDFIKAGADIVSVHCEQSSTIHLHRTINQIKSLGAKAGVVLNPGTPLTAIEYVLDAVDLVLIMSVNPGFGGQSFIESQVKKISDLRKICAERGLNPWIEVDGGVGPKNAYKVIEAGANALVAGSAVFGAPDYAEAIKGIKTSKRPE 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain C from PDB  Type:PROTEIN  Length:230
 aligned with RPE_SOLTU | Q43843 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:230
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276
            RPE_SOLTU    47 SRVDKFSKSDIIVSPSILSANFSKLGEQVKAIEQAGCDWIHVDVMDGRFVPNITIGPLVVDSLRPITDLPLDVHLMIVEPDQRVPDFIKAGADIVSVHCEQSSTIHLHRTINQIKSLGAKAGVVLNPGTPLTAIEYVLDAVDLVLIMSVNPGFGGQSFIESQVKKISDLRKICAERGLNPWIEVDGGVGPKNAYKVIEAGANALVAGSAVFGAPDYAEAIKGIKTSKRPE 276
               SCOP domains d1rpxc_ C: D-ribulose-5-phosphate 3-epimerase                                                                                                                                                                                          SCOP domains
               CATH domains 1rpxC00 C:1-230 Aldolase class I                                                                                                                                                                                                       CATH domains
           Pfam domains (1) -----------Ribul_P_3_epim-1rpxC01 C:12-214                                                                                                                                                                            ---------------- Pfam domains (1)
           Pfam domains (2) -----------Ribul_P_3_epim-1rpxC02 C:12-214                                                                                                                                                                            ---------------- Pfam domains (2)
           Pfam domains (3) -----------Ribul_P_3_epim-1rpxC03 C:12-214                                                                                                                                                                            ---------------- Pfam domains (3)
         Sec.struct. author .hhhh........eeehhh..hhhhhhhhhhhhh....eeeeeee...........hhhhhhhhhh...eeeeeee...hhhhhhhhhh....eeeee........hhhhhhhhhh...eeeeee.....hhhh........eeeee............hhhhhhhhhhhhhhhhh....eeeee.......hhhhhhh...eee..hhhh....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RIBUL_P_3_EPIME-----------------------------------------------------------------------------------------RIBUL_P_3_EPIMER_2     ---------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rpx C   1 SRVDKFSKSDIIVSPSILSANFSKLGEQVKAIEQAGCDWIHVDVMDGRFVPNITIGPLVVDSLRPITDLPLDVHLMIVEPDQRVPDFIKAGADIVSVHCEQSSTIHLHRTINQIKSLGAKAGVVLNPGTPLTAIEYVLDAVDLVLIMSVNPGFGGQSFIESQVKKISDLRKICAERGLNPWIEVDGGVGPKNAYKVIEAGANALVAGSAVFGAPDYAEAIKGIKTSKRPE 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

   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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (RPE_SOLTU | Q43843)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016857    racemase and epimerase activity, acting on carbohydrates and derivatives    Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule.
    GO:0004750    ribulose-phosphate 3-epimerase activity    Catalysis of the reaction: D-ribulose 5-phosphate = D-xylulose 5-phosphate.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006098    pentose-phosphate shunt    The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
    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:0009535    chloroplast thylakoid membrane    The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

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