Journal:Acta Cryst D:S2059798322011639
From Proteopedia
Drosophila melanogaster Frataxin: Protein Crystal and Predicted Solution Structure with Identification of the Fe-Binding RegionsAndria V. Rodrigues, Sharon Batelu, Tiara V. Hinton, John Rotondo, Lindsey Thompson, Joseph S. Brunzelle, Timothy L. Stemmler [1] Molecular Tour Recent reports from the Markley Lab (Cai et al, 2018[2]) confirmed that Fe(II) is delivered by frataxin to the scaffold in the presence of ferredoxin; ferredoxin within the pathway provides reducing equivalents for cluster assembly. Previous reports (Kondapalli et al, 2008[3]; Koebke et al, 2019[4]) confirmed the binding affinities of Fe(II) to frataxin orthologs of yeast (Saccharomyces cerevisiae) and flies (Drosophila melanogaster). In Drosophila frataxin (Dfh), which has shown increased stability relative to its orthologs, iron binds within the micromolar affinity range. Other frataxin orthologs also bind in this range and these affinities are within the range of available Fe(II) in the mitochondria. This suggests that Dfh is loaded with Fe(II) while in the cellular mitochondrial matrix. Based on the iron binding capability of Dfh with respect to Fe-S cluster assembly and its increased stability, this report characterizes the crystal and solution state structures of Dfh and highlights likely Fe-binding residues. In this study, we found that all frataxin orthologs are very similar in structure as expected from their comparative amino acid sequence alignment. However, this structural similarity does not translate to protein stability. The X-ray crystal structure of Dfh (ribbon representation), at a resolution of 1.4 Å, is a well-folded protein with a conserved αβ-sandwich motif with two α-helices, six β-sheets, and a 310-helix on the C-terminal tail. Labels for the different secondary structural elements are marked on the corresponding helix or strand (PDB ID: 7n9i). Protein charge is shown. This scene highlights the acidic patch on Dfh, and where iron is likely to bind to the protein. Remember to drag the structures with the mouse to rotate them. For example, there is orientation that corresponds to the ribbon representation. The solution structure, which is highly similar, has minor differences in the length of the N-terminal tail and β-sheets, and the helix of the C-terminal tail is absent; differences likely due to crystal packing. Potential Fe-binding residues on Dfh were identified by nuclear magnetic resonance in the presence of Fe(II). Of the 133 residues in Dfh, 8 were perturbed, beyond the threshold, in the presence of iron. The residues are predominantly acidic and in the same region as seen in frataxin orthologs. Comparison of different orthologs of the frataxin protein:
These scenes emphasize the conserved αβ-sandwich motif of frataxin across the orthologs. Orientation of iron impacted residues on the crystal structure of Dfh:
Residues perturbed upon iron addition with a δ > 1.0 (colored green, labeled, with ball and stick structure) include A26, L27, E36, and N37 on helix 1; D45 on strand 1; V55 and N56 on strand 2; and T70 on strand 3. Residues that disappeared (have line broadening beyond recognition) upon iron addition (colored red) include C28, D29, and T35 located on the helix-1; A47 on the strand 2; and D50 on the strand 1, 2 loop. These scenes are emphasizing the location of the iron-binding residues based on NMR. References
|
| ||||||||||
