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. 2020 Aug 11;9:e57081. doi: 10.7554/eLife.57081

Figure 3. Coordination environment of Sfh5-bound heme.

Figure 3.

(A) Left panel shows the surface rendering of Sfh5 in grey. Right panel shows surface view of Sfh5 clipped to expose the buried heme rendered in yellow ball and stick with protein secondary structure elements depicted in cartoon ribbon. (B) Heme bound to chain B of the Sfh5 crystal structure. The 2Fo-Fc electron density map for heme contoured at 1.5 σ is displayed as blue mesh. Residues engaged in van der Waals contacts with heme are shown as gray spheres. The side-chains of residues interacting with the propionyl groups of heme (K209 and R148) are presented as red dots. (C) Left panel: Sfh5 residues that bind heme are shown including the Fe-coordinating residues Y175 and H173. Dashed lines identify the inter-atomic distances between the indicated Sfh5 residues and cognate components of heme. Polder omit electron density map for heme is shown as green mesh (Liebschner et al., 2017), contoured at 2.5 σ. Right panel: Lateral view of the 2Fo-Fc map showing electron density associated with residues coordinating the heme iron center (contoured at 1.5σ). (D) Surface view of Sfh5 clipped to display the ligand-binding cavity. Bound heme (shown in ball and stick and colored by the element with carbons in gold) resides deep inside the cavity. Heme-coordinating residues H173 and Y175 are displayed in ball and stick mode and colored by element with carbons in light gray. Indicated access to the vacant heme coordination site from solvent is potentially controlled by conformational transitions of the K188 and K192 side chains (labeled as substrate channel, entrance displayed in ball and stick render and colored by element with carbons in green), and the side-chains of residues L224, I225 and F228 (colored by element with carbons in yellow). The surface contributed by the side chains of residues K188 and K192 is colored in green. Access channel for lipid to the internal cavity of other Sec14-like PITPs is also indicated.

Figure 3—source data 1. Fungal Sfh5 orthologs.
The S. cerevisiae Sfh5 primary sequence was used as query in a Uniprot BLAST search to identify orthologs across the fungal kingdom. Initial sequence alignments were performed using ClustalW and followed by a Sfh5 structure guided alignment of the sequences using ESCRIPT. Sequences from C. glabrata, C. albicans, C. tropicalis, C. auris, A. nidulans, A. oryzae, N. crassa, C. neoformans and Y. lipolytica were aligned. Conserved residues are highlighted in red. At bottom are identified the Sfh5 residues that: (i) correspond to the PtdIns-binding barcode common to Sec14-like PITPs (▲), (ii) that are engaged in van der Waals interactions with heme or π-π stacking interactions with the pyrrole groups of the porphyrin ring (●), (iii) engage in electrostatic or H-bond interactions with heme -- that is. the heme-binding barcode (♦) and (iv) conserved residues Lys188 and Lys192 that are poised to gate access to the empty pocket distal to the heme iron (arrows). Secondary structure elements as determined from the Sfh5 crystal structure are identified at top.