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The Open Protein Structure Annotation Network
PDB Keyword
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3dfu

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

    Title Crystal structure of Protein of Unknown Function from the 6-Phosphogluconate Dehydrogenase-Like Family (NP_601885.1) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 2.07 A resolution. To be published
    Site JCSG
    PDB Id 3dfu Target Id 377822
    Molecular Characteristics
    Source Corynebacterium glutamicum atcc 13032
    Alias Ids TPS7007,NP_601885.1 Molecular Weight 25415.17 Da.
    Residues 231 Isoelectric Point 4.54
    Sequence mqaprlrvgifddgsstvnmaekldsvghyvtvlhapedirdfelvvidahgvegyveklsafarrgqm flhtslthgitvmdpletsggivmsahpigqdrwvasaldelgetivgllvgelggsiveiaddkraql aaaltyagflstlqrdasyfldeflgdpdvtsdivmdsaqqfqalpsldeviaqydsinnpgrqrlfrd larrqaeisraqdielwaiqkedr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.07 Rfree 0.223
    Matthews' coefficent 2.25 Rfactor 0.191
    Waters 251 Solvent Content 45.30

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3dfu

    Protein Summary

    The Cgl2689 gene from Corynebacterium glutamicum ATCC 13032 encodes the protein NP_601885. The N-terminal domain, residues 1-97,  belong to the Rossmann-like (PF10727) family, as part of clan CL0063.  The C-terminal domain, residues 110-213, belong to the DUF2520 (PF10728) family. 

    The 3dfu structure (all helical) consists of two domains, shown in Fig 1. The C-terminal domain acts as a dimerization domain as shown in the dimer structure in Fig 2.

    Fig 1. 3dfu monomer structure consists of two domains.




    Fig 2. The C-terminal domains of 3dfu wrap around each other to form a dimer.

    DALI top hits for a 3dfu search are with putative oxidoreductase 3d1l (Z=15), a prephenate dehydrogenase 2f1k (Z=13), and a hydroxyacyl-CoA dehydrogenase 1f17 (Z=13). 3dfu is structurally similar to proteins in the 6-phosphogluconate dehydrogenase-like, N-terminal domain family from SCOP, including a 1-Pyrroline-5-Carboxylate reductase (PDB code: 2ahr; Z=11) and TM1727 from Thermotoga maritima (PDB code: 2i76; Z=10), which also has a topsan page.  3dfu has more sequence similarity with TM1727 than with 1-Pyrroline-5-Carboxylate reductase.  


     

    Ligand Summary

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    References

     

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