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(-) Description

Title :  THE STRUCTURE OF THE CYTOSOLIC D-RIBULOSE-5-PHOSPHATE 3-EPIMERASE FROM RICE COMPLEXED WITH SULFATE AND ZINC
 
Authors :  S. Jelakovic, G. E. Schulz
Date :  25 Jul 02  (Deposition) - 30 Jan 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  3-Epimerase, Oxidative Pentose Phosphate Pathway, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Jelakovic, S. Kopriva, K. Suss, G. E. Schulz
Structure And Catalytic Mechanism Of The Cytosolic D-Ribulose-5-Phosphate 3-Epimerase From Rice
J. Mol. Biol. V. 326 127 2003
PubMed-ID: 12547196  |  Reference-DOI: 10.1016/S0022-2836(02)01374-8

(-) Compounds

Molecule 1 - D-RIBULOSE-5-PHOSPHATE 3-EPIMERASE
    ChainsA, B
    EC Number5.1.3.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonRICE
    Organism ScientificORYZA SATIVA
    Organism Taxid4530

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:36 , ASP A:38 , HIS A:69 , ASP A:178BINDING SITE FOR RESIDUE ZN A1224
2AC2SOFTWAREGLY A:152 , GLY A:180 , GLY A:200 , SER A:201BINDING SITE FOR RESIDUE SO4 A1225
3AC3SOFTWAREHIS B:36 , ASP B:38 , HIS B:69 , ASP B:178BINDING SITE FOR RESIDUE ZN B1224
4AC4SOFTWAREGLY B:152 , GLY B:180 , GLY B:200 , SER B:201BINDING SITE FOR RESIDUE SO4 B1225

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H1Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H1Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H1Z)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBUL_P_3_EPIMER_1PS01085 Ribulose-phosphate 3-epimerase family signature 1.RPE1_ORYSJ36-50
 
  2A:35-49
B:35-49
2RIBUL_P_3_EPIMER_2PS01086 Ribulose-phosphate 3-epimerase family signature 2.RPE1_ORYSJ142-164
 
  2A:141-163
B:141-163

(-) Exons   (0, 0)

(no "Exon" information available for 1H1Z)

(-) Sequences/Alignments

Asymmetric/Biological 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:220
 aligned with RPE1_ORYSJ | Q9SE42 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:220
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
           RPE1_ORYSJ     6 AAKIAPSMLSSDFANLAAEADRMVRLGADWLHMDIMDGHFVPNLTIGAPVIQSLRKHTKAYLDCHLMVTNPSDYVEPLAKAGASGFTFHIEVSRDNWQELIQSIKAKGMRPGVSLRPGTPVEEVFPLVEAENPVELVLVMTVEPGFGGQKFMPEMMEKVRALRKKYPSLDIEVDGGLGPSTIDVAASAGANCIVAGSSIFGAAEPGEVISALRKSVEGSQ 225
               SCOP domains d1h1za_ A: D-ribulose-5-phosphate 3-epimerase                                                                                                                                                                                SCOP domains
               CATH domains 1h1zA00 A:5-224 Aldolase class I                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhh....eeeeeee...hhhhhhhhhhhh..eeeee......hhhhhhhhhhh...eeeeee....hhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------RIBUL_P_3_EPIME-------------------------------------------------------------------------------------------RIBUL_P_3_EPIMER_2     ------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h1z A   5 AAKIAPSMLSSDFANLAAEADRMVRLGADWLHMDIMDGHFVPNLTIGAPVIQSLRKHTKAYLDCHLMVTNPSDYVEPLAKAGASGFTFHIEVSRDNWQELIQSIKAKGMRPGVSLRPGTPVEEVFPLVEAENPVELVLVMTVEPGFGGQKFMPEMMEKVRALRKKYPSLDIEVDGGLGPSTIDVAASAGANCIVAGSSIFGAAEPGEVISALRKSVEGSQ 224
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with RPE1_ORYSJ | Q9SE42 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:220
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
           RPE1_ORYSJ     6 AAKIAPSMLSSDFANLAAEADRMVRLGADWLHMDIMDGHFVPNLTIGAPVIQSLRKHTKAYLDCHLMVTNPSDYVEPLAKAGASGFTFHIEVSRDNWQELIQSIKAKGMRPGVSLRPGTPVEEVFPLVEAENPVELVLVMTVEPGFGGQKFMPEMMEKVRALRKKYPSLDIEVDGGLGPSTIDVAASAGANCIVAGSSIFGAAEPGEVISALRKSVEGSQ 225
               SCOP domains d1h1zb_ B: D-ribulose-5-phosphate 3-epimerase                                                                                                                                                                                SCOP domains
               CATH domains 1h1zB00 B:5-224 Aldolase class I                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhh....eeeeeee...hhhhhhhhhhhh..eeeee......hhhhhhhhhhh...eeeeee....hhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhhhh...eeeeeeeehhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------RIBUL_P_3_EPIME-------------------------------------------------------------------------------------------RIBUL_P_3_EPIMER_2     ------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h1z B   5 AAKIAPSMLSSDFANLAAEADRMVRLGADWLHMDIMDGHFVPNLTIGAPVIQSLRKHTKAYLDCHLMVTNPSDYVEPLAKAGASGFTFHIEVSRDNWQELIQSIKAKGMRPGVSLRPGTPVEEVFPLVEAENPVELVLVMTVEPGFGGQKFMPEMMEKVRALRKKYPSLDIEVDGGLGPSTIDVAASAGANCIVAGSSIFGAAEPGEVISALRKSVEGSQ 224
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H1Z)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RPE1_ORYSJ | Q9SE42)
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:0044262    cellular 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, as carried out by individual cells.
    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:0019323    pentose catabolic process    The chemical reactions and pathways resulting in the breakdown of a pentose, any monosaccharide with a chain of five carbon atoms in the molecule.
    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:0009052    pentose-phosphate shunt, non-oxidative branch    The branch of the pentose-phosphate shunt which does not involve oxidation reactions. It comprises a series of sugar phosphate interconversions, starting with ribulose 5-P and producing fructose 6-P and glyceraldehyde 3-P.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RPE1_ORYSJ | Q9SE421h1y

(-) Related Entries Specified in the PDB File

1h1y THE STRUCTURE OF THE CYTOSOLIC D-RIBULOSE- 5-PHOSPHATE 3-EPIMERASE FROM RICE COMPLEXED WITH SULFATE