9E5G

Cryo-EM structure of Burkholderia cenocepacia orotate phosphoribosyltransferase

Summary for 9E5G

• Entry DOI: 10.2210/pdb9e5g/pdb
• EMDB information: 47526
• Descriptor: Orotate phosphoribosyltransferase, ACETATE ION (3 entities in total)
• Functional Keywords: orotic acid phosphoribosyltransferase, transferase
• Biological source: Burkholderia cenocepacia J2315
• Total number of polymer chains: 6
• Total formula weight: 159722.06

Authors

Sharma, N.,French, J.B. (deposition date: 2024-10-28, release date: 2025-02-19, Last modification date: 2025-05-21)

Primary citation

Sharma, N.,Turlington, Z.R.,Zupko, S.P.,Catoggio, M.N.,Lukacs, C.M.,Serbzhinskiy, D.,Abendroth, J.,Edwards, T.E.,Lorimer, D.D.,Barrera, G.,Willis, S.,Beyer, O.,Toay, S.,Da Li, T.,Torelli, A.T.,Hicks, K.A.,French, J.B.
Structural and kinetic analysis of distinct active and inactive states of Burkholderia cenocepacia orotate phosphoribosyltransferase.
Arch.Biochem.Biophys., 766:110332-110332, 2025

PubMed Abstract: Orotate phosphoribosyltransferase (OPRT) catalyzes the reaction that adds the pyrimidine base to the ribose in the penultimate step of the de novo biosynthesis of pyrimidine nucleotides. The OPRT structure consists of an obligate dimer, conserved throughout the phosphoribosyltransferase family. Here, we describe the structural characterization of Burkholderia cenocepacia OPRT (BcOPRT), both by X-ray crystallography and Cryo electron microscopy (Cryo-EM). While the known dimer is present in the structure of BcOPRT, a putative hexameric form was also observed by multiple methods. Analyses by chromatography, Cryo-EM, and kinetics indicate that both dimeric and hexameric forms of this enzyme are present together in solution. Comparison of the kinetics of the native protein and two variants, which were specifically designed to prevent hexamerization, reveal that only the hexameric form is enzymatically active. Collectively, these data suggest that BcOPRT may use oligomerization to control overall enzymatic activity, thus contributing to the local regulation of pyrimidine biosynthesis in this organism.

PubMed: 39938730
DOI: 10.1016/j.abb.2025.110332

Experimental method

ELECTRON MICROSCOPY (3.07 Å)