What Determines the Selectivity of Arginine Dihydroxylation by the Nonheme Iron Enzyme OrfP?

Abstract

The nonheme iron enzyme OrfP reacts with l‐Arg selectively to form the 3R,4R‐dihydroxyarginine product, which in mammals can inhibit the nitric oxide synthase enzymes involved in blood pressure control. To understand the mechanisms of dioxygen activation of l‐Arg by OrfP and how it enables two sequential oxidation cycles on the same substrate, we performed a density functional theory study on a large active site cluster model. We show that substrate binding and positioning in the active site guides a highly selective reaction through C3−H hydrogen atom abstraction. This happens despite the fact that the C3−H and C4−H bond strengths of l‐Arg are very similar. Electronic differences in the two hydrogen atom abstraction pathways drive the reaction with an initial C3−H activation to a low‐energy 5σ‐pathway, while substrate positioning destabilizes the C4−H abstraction and sends it over the higher‐lying 5π‐pathway. We show that substrate and monohydroxylated products are strongly bound in the substrate binding pocket and hence product release is difficult and consequently its lifetime will be long enough to trigger a second oxygenation cycle.

Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1

“…In an alternative pathway, the Fe III −OH species may undergo the OH‐rebound to the C21 radical site via a slightly larger barrier of 5.2 kcal mol −1 , affording to the hydroxylated substrate which is 27.6 kcal mol −1 more stable than the intermediate IC1 (Figure S13). The calculated rebound barrier is in line with previous studies [60–73] . The hydroxylated species would lead to the side product 8 through elimination (refer to Scheme 3), as observed in experiments.…”

“…Thec alculated rebound barrier is in line with previous studies. [60][61][62][63][64][65][66][67][68][69][70][71][72][73] The hydroxylated species would lead to the side product 8 through elimination (refer to Scheme 3), as observed in experiments. Clearly,t he dioxygen attack is kinetically favorable over the rebound pathway,w hile the rebound pathway is more thermodynamically favorable.Inthe situation of low concen- S3 and Figure S15).…”

Proton-coupled electron transfer reactivities of electronically divergent heme superoxide intermediates: a kinetic, thermodynamic, and theoretical study

“…By contrast, for hydrogen atom abstraction of aliphatic substrates by P450 compound I or non-heme iron dioxygenases typically values well larger than 12 are calculated. 48 Our obtained KIE value is in good agreement with the experimentally determined value of 6.7 ( Table 1 ) and hence the calculations give a similar potential energy landscape and curvature as derived from the experimental work.…”

Density Functional Theory Study into the Reaction Mechanism of Isonitrile Biosynthesis by the Nonheme Iron Enzyme ScoE

“…The Gaussian-09 software package was used for all quantum chemical calculations discussed here [55]. Following previous experience with cluster models of nonheme iron dioxygenases [53,56,57], we utilized the unrestricted B3LYP density functional method [58,59] in combination with a LANL2DZ (with electron core potential) on iron and 6-31G on the rest of the atoms: basis set BS1 [60,61]. To correct the energetics, single point calculations with the LACV3P + (with electron core potential) on iron and 6-311 + G* on the rest of the atoms were performed (basis set BS2).…”