Work

Structure of the NAD + Bound Erythrose‐4‐Phosphate Dehydrogenase ( E4PDH ) Reveals the Stabilizing Effect of Polyethylene Glycol on the Quaternary Structure

Year: 2025

Type: article

Abstract: ABSTRACT Erythrose‐4‐phosphate dehydrogenase (E4PDH, EC 1.2.1.72) from Acinetobacter baumannii ( Ab E4PDH) is an essential multifunctional enzyme. E4PDH catalyzes the first step of the deoxyxylulose‐5‐phosphate (DXP) dependent Vitamin B6 biosynthetic pathway. It utilizes nicotinamide adenine diphosphate (NAD + ) as a co‐factor while exhibiting dual catalytic activity wherein it converts (i) D‐Erythrose‐4‐phosphate to 4‐phosphoerythronate and (ii) Glyceraldehyde‐3‐phosphate to Glyceraldehyde‐1,3‐bisphosphate. An alternate function of Ab E4PDH is the capture of human transferrin (Tf) and lactoferrin (Lf) for bacterial iron acquisition. This study provides the first X‐ray crystal structures of Ab E4PDH at a resolution of 2.2 Å. The recombinant enzyme was crystallized under two different conditions with (i) 30% PEG‐400 (Crystal/Structure 1; PDB Id‐9IIL) and (ii) 1.6 M MgSO 4 (Crystal/Structure 2; PDB Id‐9IIM). The crystal structure reveals a homo‐tetramer, with an NAD + bound to each monomer. The structure from Crystal 2 contained only four sulfate ions which were located in the substrate binding sites. In contrast, Crystal 1 showed the presence of several polyethylene glycol (PEG) molecules located in the center of the tetramer contributing to its stability without disturbing co‐factor binding. The presence of PEG molecules induced a strong conformational change in the side chain of Gln213, inducing the formation of additional intermolecular contacts and enhancing the stability of the tetramer. Overall, this novel structure has not been observed with other dehydrogenases and may be unique to E4PDH. An insight into this structure would aid in the design of potential small molecule inhibitors to target its biochemical and alternate functions.

Source: Proteins Structure Function and Bioinformatics

DOI: 10.1002/prot.70083