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

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.

Abstract

The enzymes PhnY and PhnZ comprise an oxidative catabolic pathway that enables marine bacteria to use 2-aminoethylphosphonic acid as a source of inorganic phosphate. PhnZ is notable for catalyzing the oxidative cleavage of a carbon–phosphorus bond using Fe(II) and dioxygen, despite belonging to a large family of hydrolytic enzymes, the HD-phosphohydrolase superfamily. We have determined high-resolution structures of PhnZ bound to its substrate, (R)-2-amino-1-hydroxyethylphosphonate (2.1 Å), and a buffer additive, L-tartrate (1.7 Å). The structures reveal PhnZ to have an active site containing two Fe ions coordinated by four histidines and two aspartates that is strikingly similar to the carbon–carbon bond cleaving enzyme, myo-inositol-oxygenase. The exception is Y24, which forms a transient ligand interaction at the dioxygen binding site of Fe2. Site-directed mutagenesis and kinetic analysis with substrate analogs revealed the roles of key active site residues. A fifth histidine that is conserved in the PhnZ subclade, H62, specifically interacts with the substrate 1-hydroxyl. The structures also revealed that Y24 and E27 mediate a unique induced-fit mechanism whereby E27 specifically recognizes the 2-amino group of the bound substrate and toggles the release of Y24 from the active site, thereby creating space for molecular oxygen to bind to Fe2. Structural comparisons of PhnZ reveal an evolutionary connection between Fe(II)-dependent hydrolysis of phosphate esters and oxidative carbon–phosphorus or carbon–carbon bond cleavage, thus uniting the diverse chemistries that are found in the HD superfamily.

Electrochemical evidence that pyranopterin redox chemistry controls the catalysis of YedY, a mononuclear Mo enzyme

Hope Adamson a, Alexandr N. Simonov b, Michelina Kierzek c, Richard A. Rothery c, Joel H. Weiner c, Alan M. Bond b, and Alison Parkin a,1 a Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom; b School of Chemistry, Monash University, Clayton, VIC 3800, Australia; and c Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada Edited by Harry B. Gray, California Institute of Technology, Pasadena, CA, and approved October 13, 2015 (received for review August 25, 2015) http://www.pnas.org/content/112/47/14506.short A long-standing contradiction in the field of mononuclear Mo enzyme research is that small-molecule chemistry on active-site mimic compounds predicts ligand participation in the electron transfer reactions, but biochemical measurements only suggest metal-centered catalytic electron transfer.With the simultaneous measurement of substrate turnover and reversible electron transfer that is provided by Fourier-...

Rhenium(V)–oxo corrolazines: isolating redox-active ligand reactivity

Jan Paulo T. Zaragoza,a Maxime A. Sieglera and David P. Goldberg* Chem. Commun., 2015, Advance Article DOI: 10.1039/C5CC07956J Received 22 Sep 2015, Accepted 15 Oct 2015 First published online 28 Oct 2015 http://pubs.rsc.org/en/content/articlelanding/2015/cc/c5cc07956j#!divAbstract Abstract The synthesis of the first example of a third-row metallocorrolazine characterized by single crystal X-ray diffraction is reported. This ReV(O) porphyrinoid complex shows an exclusively ligand-based reactivity with strong acids and oxidizing agents. The one-electron oxidized π-radical-cation complex is capable of H-atom abstraction.

Tuning Reactivity and Selectivity in Hydrogen Atom Transfer from Aliphatic C–H Bonds to Alkoxyl Radicals: Role of Structural and Medium Effects

Michela Salamone and Massimo Bietti* Dipartimento di Scienze e Tecnologie Chimiche, Università “Tor Vergata”, Via della Ricerca Scientifica, Italy Acc. Chem. Res., Article ASAP DOI: 10.1021/acs.accounts.5b00348 Publication Date (Web): November 6, 2015 クメンパーオキシドを光で開裂させることにより、生成するクミルアルコキシルラジカルによるアルカンやアミンのC–H切断の速度定数などの情報がまとまっています。溶媒や、酸、基質の形が反応速度定数に与える影響を定量的に評価しています。酸化反応をしている方は、手元に置いておいても良いのでしょうか。

C–H Bond Oxidation Catalyzed by an Imine-Based Iron Complex: A Mechanistic Insight

Giorgio Olivo§¶, Martina Nardi§, Diego Vìdal¶, Alessia Barbieri§, Andrea Lapi§‡, Laura Gómez¶⊥, Osvaldo Lanzalunga§‡, Miquel Costas*¶, and Stefano Di Stefano*§‡ § Università degli Studi di Roma, Rome, Italy ¶ Institut de Química Computacional i Catàlisi (IQCC), Girona, Spain Inorg. Chem., 2015, 54 (21), pp 10141–10152 DOI: 10.1021/acs.inorgchem.5b01500 Publication Date (Web): October 12, 2015 A family of imine-based nonheme iron(II) complexes (LX)2Fe(OTf)2 has been prepared, characterized, and employed as C–H oxidation catalysts. Ligands LX (X = 1, 2, 3, and 4) stand for tridentate imine ligands resulting from spontaneous condensation of 2-pycolyl-amine and 4-substituted-2-picolyl aldehydes. Fast and quantitative formation of the complex occurs just upon mixing aldehyde, amine, and Fe(OTf)2 in a 2:2:1 ratio in acetonitrile solution. The solid-state structures of (L1)2Fe(OTf)(ClO4) and (L3)2Fe(OTf)2 are reported, showing a low-spin octahedral iron center, with the lig...

Oxidative Alkene Cleavage Catalysed by Manganese-Dependent Cupin TM1459 from Thermotoga maritima

van Hajnal 1 , Kurt Faber 1,2 , Helmut Schwab 1,3 , Mélanie Hall 2,* and Kerstin Steiner 1,* a acib, Austrian Centre of Industrial Biotechnology GmbH, Petersgasse 14, 8010 Graz, Austria Fax: ( + 43)-316-873-9302; phone: ( + 43)-316-873-9346; e-mail: kerstin.steiner@acib.at b Department of Chemistry, University of Graz, Heinrichstraße 28, 8010 Graz, Austria Fax: ( + 43)-316-380-9840; phone: ( + 43)-316-380-5479; e-mail: melanie.hall@uni-graz.at c Institute of Molecular Biotechnology, TU Graz, Petersgasse 14, 8010 Graz, Austria Adv .S ynth. Catal. 2015 , 357 , 3 309 –3 316 DOI: 10.1002/adsc.201500608 Abstract A novel biocatalytic oxidative alkene cleavage activity was identified in protein TM1459 from Thermotoga maritima , a so far uncharacterised metalloprotein with a cupin fold, which preferentially binds manganese (over iron and zinc). Various styrene derivat...

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