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The Open Protein Structure Annotation Network
PDB Keyword
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3oz2

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

    Title Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids. J.Mol.Biol. 404 403-417 2010
    Site JCSG
    PDB Id 3oz2 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1766,NP_393992.1, BIG_349, PF04820, 87985
    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 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.35 Rfactor 0.1530
    Waters
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    Solvent Content 47.55

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3oz2
    1. Insights into Substrate Specificity of Geranylgeranyl Reductases Revealed by the Structure of Digeranylgeranylglycerophospholipid Reductase, an Essential Enzyme
    Q Xu, T Eguchi, II Mathews, CL Rife, HJ Chiu - Journal of molecular , 2010 - Elsevier
     
    2. CbrA Is a Flavin Adenine Dinucleotide Protein That Modifies the Escherichia coli Outer Membrane and Confers Specific Resistance to Colicin M
    S Helbig, K Hantke, M Ammelburg - Journal of Bacteriology, 2012 - Am Soc Microbiol
     
    3. Structure and mutation analyses of archaeal geranylgeranyl reductase
    D Sasaki, M Fujihashi, Y Iwata, M Murakami - Journal of molecular , 2011 - Elsevier
     

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    Protein Summary

    Ta0516 gene from Thermoplasma acidophilum encodes the NP_393992 protein, a digeranyl glycerophospholipid reductase (member of COG0644 and PF01494). Based on genomic context, Ta0516 is functionally linked (score 0.95) with its neighbor, Ta0517, a putative ferredoxin.

    The overall fold of 3cgv, as shown in Figure 1, is quite common among many different types of reductases, including the location of the FAD binding site. It is an alpha/beta class protein, and belongs to the SCOP family FAD/NAD-linked reductases. DALI top hits are with the halogenase 3e1t (Z=35), the para-hydroxybenzoate hydrolase 1ykj (Z=29) and the RDME protein 3ihg (Z=28).


    Figure 1. 3cgv exists as a monomer in the crystallographic asymmetric unit.

    The enzyme geranylgeranyl reductase catalyzes the reduction of geranylgeranyl diphosphate (Fig 2) to phytyl diphosphate (ref 1). 3cgv may be a multifunctional enzyme capable of catalyzing the reduction of geranylgeranyl-chlorophyll into phytyl-chlorophyll in addition to the reduction of geranylgeranyl diphosphate into phytyl diphosphate. 3cgv may also have a role in plastid development.


    Figure 2. Geranylgeranyl diphospate (GGPP).

    3cgv contains a long unknown ligand found near the conserved FAD binding site (Fig 3).


    Figure 3. Probable 3cgv active site location with FAD and UNL density shown. Electron density is 2Fo-Fc map, contoured at 1 sigma.


    Figure 4. GGPP molecule modeled into the putative active site.


    Figure 5. 3cgv structure, with GGPP depicted as spheres and FAD as sticks, showing that part of the GGPP molecule is surface accessible.

    Ligand Summary

    An unknown ligand is modeled in the putative active site near a bound FAD. See summary for more information.

    References

    Reviews

    References

     

    No references found.

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