Fig. 5: Structural analysis of hXRN1x-pAp complex. | Communications Biology

Fig. 5: Structural analysis of hXRN1x-pAp complex.

From: Characterization of exoribonuclease XRN1 as a cancer target and identification of adenosine-3’,5’-bisphosphate as a potent enzyme inhibitor

Fig. 5: Structural analysis of hXRN1x-pAp complex.

a Ribbon representation of hXRN1x (cyan) – pAp (blue stick) structure. Magnesium ions represented by gray spheres. b 2Fo-Fc (blue mesh, 1.0 σ) and c omit Fo-Fc (green/red mesh, +/− 3.0 σ) electron density maps of pAp unambiguously confirm the presence of the ligand in the XRN1 active site. d A close view of the XRN1-pAp binding site including XRN1 residues that interact directly with phosphate moieties of the ligand. Magenta dashes = 5’ phosphate interactions; yellow dashes = 3’ phosphate “up” orientation interactions; orange dashes = 3’ phosphate “down” orientation interactions; protein view is similar to (b, c). e Superposition of hXRN1x-pAp and Drosophila XRN1-DNA (PDB code 2Y35; gray) structures. Base rings are aligned while shifts are seen for ribose and phosphate groups. f Superposition of hXRN1x-pAp and C. elegans XRN2 (PDB code 7OPK; green) shows good overall structural similarity. g Residue differences (stick representation) in the hXRN1x and XRN2 active sites do not directly interact with pAP. h Comparison of hXRN1x-pAp (3’ “up” confirmation) and mDXO-pAp (PDB code 6AIX; pink) shows conservation of pAp orientation despite lack of structural similarity between proteins.

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