6ENZ

Crystal structure of mouse GADL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

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    This is version 1.1 of the entry. See complete history


    Literature

    Structure of the mouse acidic amino acid decarboxylase GADL1.

    Raasakka, A.Mahootchi, E.Winge, I.Luan, W.Kursula, P.Haavik, J.

    (2018) Acta Crystallogr F Struct Biol Commun 74: 65-73

    • DOI: 10.1107/S2053230X17017848
    • Primary Citation of Related Structures:  
      6ENZ

    • PubMed Abstract: 
    • Pyridoxal 5'-phosphate (PLP) is a ubiquitous cofactor in various enzyme classes, including PLP-dependent decarboxylases. A recently discovered member of this class is glutamic acid decarboxylase-like protein 1 (GADL1), which lacks the activity to decarboxylate glutamate to γ-aminobutyrate, despite its homology to glutamic acid decarboxylase ...

      Pyridoxal 5'-phosphate (PLP) is a ubiquitous cofactor in various enzyme classes, including PLP-dependent decarboxylases. A recently discovered member of this class is glutamic acid decarboxylase-like protein 1 (GADL1), which lacks the activity to decarboxylate glutamate to γ-aminobutyrate, despite its homology to glutamic acid decarboxylase. Among the acidic amino acid decarboxylases, GADL1 is most similar to cysteine sulfinic acid decarboxylase (CSAD), but the physiological function of GADL1 is unclear, although its expression pattern and activity suggest a role in neurotransmitter and neuroprotectant metabolism. The crystal structure of mouse GADL1 is described, together with a solution model based on small-angle X-ray scattering data. While the overall fold and the conformation of the bound PLP are similar to those in other PLP-dependent decarboxylases, GADL1 adopts a more loose conformation in solution, which might have functional relevance in ligand binding and catalysis. The structural data raise new questions about the compactness, flexibility and conformational dynamics of PLP-dependent decarboxylases, including GADL1.


      Organizational Affiliation

      Department of Biomedicine, University of Bergen, Jonas Lies Vei 91, 5009 Bergen, Norway.



    Macromolecules
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    Entity ID: 1
    MoleculeChainsSequence LengthOrganismDetailsImage
    Acidic amino acid decarboxylase GADL1A, B530Mus musculusMutation(s): 0 
    Gene Names: Gadl1
    EC: 4.1.1.11 (UniProt), 4.1.1.29 (UniProt)
    UniProt
    Find proteins for Q80WP8 (Mus musculus)
    Explore Q80WP8 
    Go to UniProtKB:  Q80WP8
    Entity Groups  
    Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
    UniProt GroupQ80WP8
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PLP
    Query on PLP

    Download Ideal Coordinates CCD File 
    C [auth A],
    D [auth B]
    PYRIDOXAL-5'-PHOSPHATE
    C8 H10 N O6 P
    NGVDGCNFYWLIFO-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.00 Å
    • R-Value Free: 0.288 
    • R-Value Work: 0.235 
    • R-Value Observed: 0.238 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 137.43α = 90
    b = 80.64β = 117.85
    c = 128.51γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    XDSdata scaling
    PHASERphasing

    Structure Validation

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    Ligand Structure Quality Assessment 



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2018-01-03
      Type: Initial release
    • Version 1.1: 2018-04-18
      Changes: Data collection, Database references