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The Open Protein Structure Annotation Network
PDB Keyword
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3qc3

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of a D-ribulose-5-phosphate-3-epimerase (NP_954699) from HOMO SAPIENS at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 3qc3 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS29784,NP_954699.1, 326041
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.48 Rfactor 0.1644
    Waters
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    Solvent Content 50.48

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3qc3

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    Protein Summary

    Crystal structure of the human ribulose-5-phosphate-3-epimerase at 2.20 A resolution

    This human protein (UniProt Q96AT9 (RPE_HUMAN)) is annotated as a ribulose-5-phosphate-3-epimerase isoform 1 (RPE, canonical sequence) belonging to the Pfam family PF00834 of ribulose-phosphate-3-epimerase family.

    This protein is involved in the critical Pentose Phosphate Pathway (PPP) and is involed in the conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate.

    This family has 1995 proteins from 917 species, out of which there are 213 proteins from 146 eukaryotic species, including 20 mammalian proteins (6 humans and 6 mouse proteins).

    This is the first crystal structure of a mammalian RPE, although crystal structures of RPE proteins from potato (Ref1), rice (Ref2), Synechocystis (Ref3), Plasmodium falciparum (Ref4) and S. pyogenes (Ref5) have been determined previously. They belong to the TM barrel superfamily of proteins. The closest other RPE to the human RPE whose structure has been solved is that from rice at ~51% sequence identity, PDB 1H1Y. The potato and Synechocystis areof ~38 sequence identity.

    The catalytic site in these proteins from different organisms is conserved and includes 2 His and 2 Asp residues. However, the only other  structures which showed a metal bound at the active site are the  ones from S. pyogenes (which also had an inhibitor bound) and P. falciparum.  Our structure (below) also has metal bound (this site has been modeled using partially occupied zinc, nickel and iron. The basis for modeling the 3 metals is from fluorescence excitation scans and calculation of anomalous difference Fourier maps calculated from x-ray diffraction data below and above the excitation energies of these metals, further details below). There is additional density at the putative active site, which has been modeled as glycerol from the crystallization and could be substrate mimic. This structure provides another  model to validate the protein-metal interactions that facilitate biochemistry of this enzyme.

    Fig1_monomer.png

    The protein is present as a dimer in the asymmetric unit of the unit cell in the crystal structure:

    Fig2_dimer.png

    Active site structure with bound metal (partially occupied zinc, nickel and iron, see details below for identification and characterization of metal):

    Fig3_activesite.pngFig4_activesitezoom.png

     

     

    Procedure for metal identification:

     

     

    Further detailed analysis is being done.

    References:

    1. Structure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts. Kopp J, Kopriva S, Süss KH, Schulz GE. J Mol Biol. 1999 Apr 9;287(4):761-71.PMID: 10191144

    2. Structure and catalytic mechanism of the cytosolic D-ribulose-5-phosphate 3-epimerase from rice. Jelakovic S, Kopriva S, Süss KH, Schulz GE. J Mol Biol. 2003 Feb 7;326(1):127-35.PMID: 12547196

    3. Structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 A resolution. Wise EL, Akana J, Gerlt JA, Rayment I. Acta Crystallogr D Biol Crystallogr. 2004 Sep;60(Pt 9):1687-90. Epub 2004 Aug 26.PMID:153339554

    4. Structure of a ribulose 5-phosphate 3-epimerase from Plasmodium falciparum. Caruthers J, Bosch J, Buckner F, Van Voorhis W, Myler P, Worthey E, Mehlin C, Boni E, DeTitta G, Luft J, Lauricella A, Kalyuzhniy O, Anderson L, Zucker F, Soltis M, Hol WG. Proteins. 2006 Feb 1;62(2):338-42.PMID: 16304640

    5. D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily. Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt PC, Almo SC, Gerlt JA. Biochemistry. 2006

    Ligand Summary

    3 metals have been modeled at the putative active site with partial occupancies: zinc (ZN) at 0.45 occupancy, nickel (NI) and 0.30 occupancy and iron (FE) at 0.25 occupancy.

    Glycerol (GOL) has also been modeled at the putative active site.

    Reviews

    References

     

    No references found.

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