Identification, characterization, and structure of a tRNA splicing enzyme RNA 5′-OH kinase from the pathogenic fungi Mucorales

Structure of Rhizopus RNA kinase in complex with GDP•Mg²⁺. (A) Stereo view of an omit electron density map (gray mesh, contoured at 2σ) covering the GDP and Mg²⁺•(H₂O)₄ ligands in the kinase active site. GDP is rendered as a stick model with gray carbons and yellow phosphorus atoms. A magnesium ion engaging the GTP β phosphate is depicted as a green sphere. Waters occupying five of the six positions in the octahedral magnesium coordination complex are rendered as red spheres. (B) The tertiary structure of RazKIN is shown as a cartoon trace with β-strands colored magenta, α-helices colored cyan, and a 3₁₀ helix colored blue. The helix-loop-helix “lid” overlying the GDP and the P-loop that engages the GDP phosphates are indicated in black font. The “G-loop” that engages the guanine nucleobase is indicated in blue font. Hydrogen bonds to the guanine from Ser146 in the G-loop are denoted by dashed lines.