8UW6

Acetylornithine deacetylase from Escherichia coli, di-zinc form.

Summary for 8UW6

• Entry DOI: 10.2210/pdb8uw6/pdb
• Related: 7RSF
• Descriptor: Acetylornithine deacetylase, ZINC ION, SULFATE ION, ... (6 entities in total)
• Functional Keywords: acetylornithine deacetylase, arge, m20 peptidase, structural genomics, center for structural biology of infectious diseases, csbid, hydrolase
• Biological source: Escherichia coli str. K-12 substr. MG1655
• Total number of polymer chains: 4
• Total formula weight: 172949.26

Authors

Osipiuk, J.,Endres, M.,Kelley, E.,Becker, D.P.,Joachimiak, A.,Center for Structural Biology of Infectious Diseases (CSBID) (deposition date: 2023-11-06, release date: 2024-05-29, Last modification date: 2024-08-07)

Primary citation

Kelley, E.H.,Osipiuk, J.,Korbas, M.,Endres, M.,Bland, A.,Ehrman, V.,Joachimiak, A.,Olsen, K.W.,Becker, D.P.
N alpha-acetyl-L-ornithine deacetylase from Escherichia coli and a ninhydrin-based assay to enable inhibitor identification.
Front Chem, 12:1415644-1415644, 2024

PubMed Abstract: Bacteria are becoming increasingly resistant to antibiotics, therefore there is an urgent need for new classes of antibiotics to fight antibiotic resistance. Mammals do not express -acetyl-L-ornithine deacetylase (ArgE), an enzyme that is critical for bacterial survival and growth, thus ArgE represents a promising new antibiotic drug target, as inhibitors would not suffer from mechanism-based toxicity. A new ninhydrin-based assay was designed and validated that included the synthesis of the substrate analog , -di-methyl -acetyl-L-ornithine (k/K = 7.32 ± 0.94 × 10 Ms). This new assay enabled the screening of potential inhibitors that absorb in the UV region, and thus is superior to the established 214 nm assay. Using this new ninhydrin-based assay, captopril was confirmed as an ArgE inhibitor (IC = 58.7 μM; K = 37.1 ± 0.85 μM), and a number of phenylboronic acid derivatives were identified as inhibitors, including 4-(diethylamino)phenylboronic acid (IC = 50.1 μM). Selected inhibitors were also tested in a thermal shift assay with ArgE using SYPRO Orange dye against ArgE to observe the stability of the enzyme in the presence of inhibitors (captopril K = 35.9 ± 5.1 μM). The active site structure of di-Zn ArgE was confirmed using X-ray absorption spectroscopy, and we reported two X-ray crystal structures of ArgE. In summary, we describe the development of a new ninhydrin-based assay for ArgE, the identification of captopril and phenylboronic acids as ArgE inhibitors, thermal shift studies with ArgE + captopril, and the first two published crystal structures of ArgE (mono-Zn and di-Zn).

PubMed: 39055043
DOI: 10.3389/fchem.2024.1415644

Experimental method

X-RAY DIFFRACTION (1.8 Å)