Crystal structure of PhnZ in complex with substrate reveals a di-iron oxygenase mechanism for catabolism of organophosphonates

Abstract

Significance Inorganic phosphate (Pi) is an essential component of many biological molecules and thus is required by all life forms. However, soluble Pi is typically at low abundance in the environment. To compensate, microbes have evolved unique carbon–phosphorus-bond cleaving reactions to use organophosphonates as an alternative source of Pi. The marine-derived enzyme PhnZ utilizes a new oxidative mechanism for CP bond cleavage involving iron and molecular oxygen. The three-dimensional structure of PhnZ reveals unique active site features that contribute to catalysis of CP bond cleavage and substrate specificity, as well as an evolutionary link between phosphodiester bond hydrolysis and oxidative bond cleavage. This evolutionary link likely reflects the ancient origins of organophosphonates in the environment.

A growing family of O2 activating dinuclear iron enzymes with key catalytic diiron(III)-peroxo intermediates: Biological systems and chemical models

“…Among the recent discoveries, can be found: -The MiaE tRNA monooxygenase, isolated from Salmonella typhimurium, that is responsible for the post-translational tRNA modification by allylic hydroxylation of 2-methylthio-N-6-isopentyladenosine [126,127]. -The PhnZ HD phosphohydroxylase, that catalyzes the conversion of 2-aminoethylphosphonate to 2-amino-1-hydroxyethylphosphonate (a phosphate source for aquatic bacteria) [128,129]. -The 5-demethoxyubiquinone hydroxylase, also known as Clock-1 (clk-1), that is apparently responsible for slowing down the aging process in mammalian organisms [130].…”

Determination of the Absolute Configuration of (−)‐Hydroxynitrilaphos and Related Biosynthetic Questions

“…33 Mosher esterification could not be used to determine the ee of the obtained sample due to racemization under the necessary reaction conditions . Reduction of the nitrile using BH 3 ⋅ THF, followed by removal of the phosphorus protecting groups with 6 m HCl gave (−)‐2‐amino‐1‐hydroxyethylphosphonic acid [(−)‐1‐OH‐2‐AEP, 26 ], another abundant phosphonic acid natural product, of known configuration. ( R )‐1‐OH‐2‐AEP ( ee >99 %) has an optical rotation of [ α ] =−36.8 (in H 2 O), while we observed [ α ] =−25.7 (in H 2 O) for a sample obtained from (+)‐ 24 .…”

“…[ α ] =−25.7 ( c= 0.75 in D 2 O); δ H (400.27 MHz, D 2 O)=4.09–3.95 (m, 1 H, CH‐P), 3.31 (AB‐system, 2 H, CH 2 , A‐part: m, B‐part: m); δ P (162.03 MHz, D 2 O)=17.66 (s) …”

“…Then, CDCl 3 (1 mL) was added, the solution was filtered over cotton and evaporated similarly.F inally,t he obtained sample was dried in vacuo to constant weight (1 h). The desired product 28 was obtained as glassy solid (8 mg [16] Synthesis of the 13 C-labeled substances [1-13 C]Chloroacetonitrile ([1-13 C]36): [40] Sodium [ 13 C]cyanide (99 % 13 C, 1.12 g, 22.4 mmol) and paraformaldehyde (691 mg, 23.0 mmol) were dissolved in water (8 mL) and the pH of the solution was adjusted to 2.0 with H 2 SO 4 (conc.). The mixture was stirred at 0 8Cf or 2h before addition of CH 2 Cl 2 (100 mL).…”

“…[14] Mycothiol-dependent transferaseg enes suggest mycothiol as source of N-acetylcysteine in phosphonocystoximates,s imilart oac ommon xenobiotic detoxification strategy in Actinobacteria. [15] An additionally identified a-ketoglutarate dependent/non-hemeF e II dioxygenase showing sequence similarity to PhnY*, [16,17] was suggested to be responsible for a-hydroxylation next to the phosphorus atom in hydroxynitrilaphos andh ydroxyphosphonocystoximate. [13] Despite thesef irst findings, many questions concerning the structure and biosynthesis of these fascinating new compounds have remained elusive.…”