The Open Protein Structure Annotation Network
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    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 382454
    Molecular Characteristics
    Source Thermoplasma acidophilum dsm 1728
    Alias Ids TPS1766,NP_393992.1, BIG_349, PF04820, 87985 Molecular Weight 43350.77 Da.
    Residues 396 Isoelectric Point 6.99
    Sequence metydvlvvgggpggstaaryaakyglktlmiekrpeigspvrcgeglskgilneadikadrsfianev kgariygpsekrpiilqsekagnevgyvlerdkfdkhlaalaakagadvwvkspalgvikengkvagak irhnneivdvrakmviaadgfesefgrwaglksvilarndiisalqyrminvdvdpdytdfylgsiapa gyiwvfpkgegmanvgigssinwihnrfelknyldrfienhpglkkgqdiqlvtggvsvskvkmpitmp glmlvgdaarlidpitgggianaivsgmyaaqvtkeaiesndyspqmmqkyeklikerferkhlrnwva keklamlsddtldklvdivseqvlttisveailkaiaekypevvkeledli
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.60 Rfree 0.1706
    Matthews' coefficent 2.35 Rfactor 0.1530
    Waters 336 Solvent Content 47.55

    Ligand Information


    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

    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.





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