27HH

Crystal structure and ligand-binding characterization of Orotidine-5'-phosphate decarboxylase from Fusobacterium nucleatum

Summary for 27HH

• Entry DOI: 10.2210/pdb27hh/pdb
• Descriptor: Orotidine 5'-phosphate decarboxylase (2 entities in total)
• Functional Keywords: omp decarboxylase, tim barrel, pyrimidine biosynthesis, fusobacterium nucleatum, lyase
• Biological source: Fusobacterium nucleatum
• Total number of polymer chains: 2
• Total formula weight: 53263.22

Authors

Kim, B.,Hwang, J.,Do, H.,Lee, J.H. (deposition date: 2026-06-01, release date: 2026-08-19)

Primary citation

Kim, B.,Hwang, J.,Shim, Y.S.,Do, H.,Lee, J.H.
Structural insights into UMP recognition and ligand specificity of orotidine 5'-Monophosphate decarboxylase from Fusobacterium nucleatum.
Biochem.Biophys.Res.Commun., 832:154388-154388, 2026

PubMed Abstract: Orotidine-5'-phosphate decarboxylase (OMP decarboxylase; ODCase) catalyzes a key step in de novo pyrimidine biosynthesis by converting orotidine-5'-monophosphate to uridine-5'-monophosphate. Despite its essential metabolic role, the structural basis underlying substrate recognition and binding dynamics in ODCase from Fusobacterium nucleatum (FnODCase) remains poorly understood. In the present study, we determined the crystal structure of FnODCase at 1.76 Å resolution in the P 1 2 1 space group, with R and R values of 0.21 and 0.23, respectively. To investigate the ligand specificity of FnODCase, we performed isothermal titration calorimetry using three nucleotides that share a pyrimidine ring: cytidine 5'-monophosphate, thymidine 5'-monophosphate, and uridine 5'-monophosphate. The ITC data showed that FnODCase selectively recognized only UMP, confirming its high specificity for the uridine moiety. Notably, structural comparisons between the apo form and UMP-bound models revealed potential conformational changes in the loop regions surrounding the active site. These structural insights are expected to inform the future development of selective antimicrobial agents against F. nucleatum.

PubMed: 42561628
DOI: 10.1016/j.bbrc.2026.154388

Experimental method

X-RAY DIFFRACTION (1.76 Å)