Structural Insights into Ligand-Induced Conformational Changes in Adenine Phosphoribosyl Transferase from Fusobacterium nucleatum

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Background: Adenine phosphoribosyltransferase (APRT) is an enzyme that facilitates adenosine monophosphate (AMP) biosynthesis by transferring a phosphoribosyl group to adenine using phosphoribosyl pyrophosphate as a donor. While the human enzyme is well characterized, structural insights into bacterial APRTs remain limited. Fusobacterium nucleatum is associated with periodontal disease, yet its APRT enzyme (FnAPRT) has not been structurally investigated. Objective: This study aimed to examine the crystal structure of FnAPRT and ligand-induced conformational changes to understand its enzymatic and substrate recognition mechanisms. Methods: The FnAPRT protein was heterologously expressed in Escherichia coli, followed by initial purification using nickel-charged affinity resin chromatography and further purification through size-exclusion chromatography. The FnAPRT structure was resolved using X-ray crystallography and compared with that of E. coli APRT (EcAPRT), exhibiting the highest amino acid sequence similarity among bacterial APRT structures. Results: AMP and phosphate (PO4) were observed in the active site of FnAPRT. Significant differences in ligand positioning were observed between the AMP-PO4-bound structures of FnAPRT and EcAPRT. Structural shifts induced by AMP-PO4 binding were detected. The Arg78 and Lys82 residues from the alternate subunit occupied the PO4 site in the absence of ligands, but they interacted with PO4 upon AMP-PO4 binding. Structural comparison of the AMP-PO4-bound FnAPRT with that of the adenine-bound EcAPRT highlighted variations in the adenine-binding site and associated structural changes. Discussion: Structural comparison of the AMP-PO4-bound FnAPRT with that of the adeninebound EcAPRT highlighted variations in the adenine-binding site and the associated structural changes. Conclusion: The AMP-PO4-bound FnAPRT exhibited distinct ligand-binding modes despite sharing a high sequence similarity with EcAPRT. The structures demonstrated ligand movement during bacterial APRT reactions.

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