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(-) Description

Title :  CRYSTAL STRUCTURE OF HRPE
 
Authors :  W. G. Liang, S. Y. Ouyang, N. Shaw, A. Joachimiak, R. G. Zhang, Z. J. Liu
Date :  16 Sep 10  (Deposition) - 09 Mar 11  (Release) - 09 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Iron Binding, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. G. Liang, S. Y. Ouyang, N. Shaw, A. Joachimiak, R. G. Zhang, Z. J. Liu
Conversion Of D-Ribulose 5-Phosphate To D-Xylulose 5-Phosphate: New Insights From Structural And Biochemical Studies On Human Rpe
Faseb J. V. 25 497 2011
PubMed-ID: 20923965  |  Reference-DOI: 10.1096/FJ.10-171207

(-) Compounds

Molecule 1 - RIBULOSE-PHOSPHATE 3-EPIMERASE
    ChainsA, B
    EC Number5.1.3.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRPE, HUSSY-17
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymD-RIBULOSE-5-PHOSPHATE 3-EPIMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1FE22Ligand/IonFE (II) ION
2XPE6Ligand/Ion3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:35 , ASP A:37 , HIS A:70 , ASP A:175 , HOH A:258 , HOH A:266BINDING SITE FOR RESIDUE FE2 A 229
2AC2SOFTWAREGLY A:4 , LYS A:6 , ASP A:32 , ASP A:171 , MET A:193BINDING SITE FOR RESIDUE XPE A 230
3AC3SOFTWAREPRO A:121 , MET A:153 , HOH A:325BINDING SITE FOR RESIDUE XPE A 231
4AC4SOFTWAREHIS A:184 , LYS A:185 , HOH A:238BINDING SITE FOR RESIDUE XPE A 232
5AC5SOFTWAREHIS B:35 , ASP B:37 , HIS B:70 , ASP B:175 , HOH B:256 , HOH B:261BINDING SITE FOR RESIDUE FE2 B 229
6AC6SOFTWAREGLY B:4 , LYS B:6 , ASP B:32 , PHE B:66 , ASP B:171BINDING SITE FOR RESIDUE XPE B 230
7AC7SOFTWAREGLN B:63 , GLY B:87 , ALA B:88 , GLY B:112BINDING SITE FOR RESIDUE XPE B 231
8AC8SOFTWAREGLU B:126 , TRP B:162BINDING SITE FOR RESIDUE XPE B 232

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OVP)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:148 -Gly A:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OVP)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBUL_P_3_EPIMER_1PS01085 Ribulose-phosphate 3-epimerase family signature 1.RPE_HUMAN34-48
 
  2A:34-48
B:34-48
2RIBUL_P_3_EPIMER_2PS01086 Ribulose-phosphate 3-epimerase family signature 2.RPE_HUMAN138-160
 
  2A:138-160
B:138-160

(-) Exons   (0, 0)

(no "Exon" information available for 3OVP)

(-) 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:221
 aligned with RPE_HUMAN | Q96AT9 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:221
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
            RPE_HUMAN     4 GCKIGPSILNSDLANLGAECLRMLDSGADYLHLDVMDGHFVPNITFGHPVVESLRKQLGQDPFFDMHMMVSKPEQWVKPMAVAGANQYTFHLEATENPGALIKDIRENGMKVGLAIKPGTSVEYLAPWANQIDMALVMTVEPGFGGQKFMEDMMPKVHWLRTQFPSLDIEVDGGVGPDTVHKCAEAGANMIVSGSAIMRSEDPRSVINLLRNVCSEAAQKR 224
               SCOP domains d3ovpa_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhh..eeeee.hhh.hhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhh...eeeee......hhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------RIBUL_P_3_EPIME-----------------------------------------------------------------------------------------RIBUL_P_3_EPIMER_2     ---------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ovp A   4 GCKIGPSILNSDLANLGAECLRMLDSGADYLHLDVMDGHFVPNITFGHPVVESLRKQLGQDPFFDMHMMVSKPEQWVKPMAVAGANQYTFHLEATENPGALIKDIRENGMKVGLAIKPGTSVEYLAPWANQIDMALVMTVEPGFGGQKFMEDMMPKVHWLRTQFPSLDIEVDGGVGPDTVHKCAEAGANMIVSGSAIMRSEDPRSVINLLRNVCSEAAQKR 224
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with RPE_HUMAN | Q96AT9 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:222
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  
            RPE_HUMAN     4 GCKIGPSILNSDLANLGAECLRMLDSGADYLHLDVMDGHFVPNITFGHPVVESLRKQLGQDPFFDMHMMVSKPEQWVKPMAVAGANQYTFHLEATENPGALIKDIRENGMKVGLAIKPGTSVEYLAPWANQIDMALVMTVEPGFGGQKFMEDMMPKVHWLRTQFPSLDIEVDGGVGPDTVHKCAEAGANMIVSGSAIMRSEDPRSVINLLRNVCSEAAQKRS 225
               SCOP domains d3ovpb_ B: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --Ribul_P_3_epim-3ovpB01 B:6-204                                                                                                                                                                         --------------------- Pfam domains (1)
           Pfam domains (2) --Ribul_P_3_epim-3ovpB02 B:6-204                                                                                                                                                                         --------------------- Pfam domains (2)
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhh..eeeee.hhh.hhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhh...eeeee......hhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------RIBUL_P_3_EPIME-----------------------------------------------------------------------------------------RIBUL_P_3_EPIMER_2     ----------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ovp B   4 GCKIGPSILNSDLANLGAECLRMLDSGADYLHLDVMDGHFVPNITFGHPVVESLRKQLGQDPFFDMHMMVSKPEQWVKPMAVAGANQYTFHLEATENPGALIKDIRENGMKVGLAIKPGTSVEYLAPWANQIDMALVMTVEPGFGGQKFMEDMMPKVHWLRTQFPSLDIEVDGGVGPDTVHKCAEAGANMIVSGSAIMRSEDPRSVINLLRNVCSEAAQKRS 225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OVP)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RPE_HUMAN | Q96AT9)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RPE_HUMAN | Q96AT93ovq 3ovr 3qc3

(-) Related Entries Specified in the PDB File

3ovq 3ovr