scholarly journals Can a Mononuclear Iron(III)‐Superoxo Active Site Catalyze the Decarboxylation of Dodecanoic Acid in UndA to Produce Biofuels?

2019 ◽  
Vol 26 (10) ◽  
pp. 2233-2242 ◽  
Author(s):  
Yen‐Ting Lin ◽  
Agnieszka Stańczak ◽  
Yulian Manchev ◽  
Grit D. Straganz ◽  
Sam P. Visser
Keyword(s):  
Active Site ◽  
Dodecanoic Acid ◽  
Mononuclear Iron

scholarly journals Roles of key active-site residues in flavocytochrome P450 BM3

1999 ◽  
Vol 339 (2) ◽  
pp. 371-379 ◽  
Author(s):  
Michael A. NOBLE ◽  
Caroline S. MILES ◽  
Stephen K. CHAPMAN ◽  
Dominikus A. LYSEK ◽  
Angela C. MACKAY ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Fatty Acid ◽  
Fatty Acid Oxidation ◽  
Active Site ◽  
Side Chain ◽  
Acid Oxidation ◽  
Dodecanoic Acid ◽  
Wild Type ◽  
Active Site Residues ◽  
P450 Bm3

The effects of mutation of key active-site residues (Arg-47, Tyr-51, Phe-42 and Phe-87) in Bacillus megaterium flavocytochrome P450 BM3 were investigated. Kinetic studies on the oxidation of laurate and arachidonate showed that the side chain of Arg-47 contributes more significantly to stabilization of the fatty acid carboxylate than does that of Tyr-51 (kinetic parameters for oxidation of laurate: R47A mutant, Km 859 µM, kcat 3960 min-1; Y51F mutant, Km 432 µM, kcat 6140 min-1; wild-type, Km 288 µM, kcat 5140 min-1). A slightly increased kcat for the Y51F-catalysed oxidation of laurate is probably due to decreased activation energy (ΔG‡) resulting from a smaller ΔG of substrate binding. The side chain of Phe-42 acts as a phenyl ‘cap ’ over the mouth of the substrate-binding channel. With mutant F42A, Km is massively increased and kcat is decreased for oxidation of both laurate (Km 2.08 mM, kcat 2450 min-1) and arachidonate (Km 34.9 µM, kcat 14620 min-1; compared with values of 4.7 µM and 17100 min-1 respectively for wild-type). Amino acid Phe-87 is critical for efficient catalysis. Mutants F87G and F87Y not only exhibit increased Km and decreased kcat values for fatty acid oxidation, but also undergo an irreversible conversion process from a ‘fast ’ to a ‘slow ’ rate of substrate turnover [for F87G (F87Y)-catalysed laurate oxidation: kcat ‘fast ’, 760 (1620) min-1; kcat ‘slow ’, 48.0 (44.6) min-1; kconv (rate of conversion from fast to slow form), 4.9 (23.8) min-1]. All mutants showed less than 10% uncoupling of NADPH oxidation from fatty acid oxidation. The rate of FMN-to-haem electron transfer was shown to become rate-limiting in all mutants analysed. For wild-type P450 BM3, the rate of FMN-to-haem electron transfer (8340 min-1) is twice the steady-state rate of oxidation (4100 min-1), indicating that other steps contribute to rate limitation. Active-site structures of the mutants were probed with the inhibitors 12-(imidazolyl)dodecanoic acid and 1-phenylimidazole. Mutant F87G binds 1-phenylimidazole > 10-fold more tightly than does the wild-type, whereas mutant Y51F binds the haem-co-ordinating fatty acid analogue 12-(imidazolyl)dodecanoic acid > 30-fold more tightly than wild-type.

scholarly journals Coordination and conformational isomers in mononuclear iron complexes with pertinence to the [FeFe] hydrogenase active site

2014 ◽  
Vol 43 (11) ◽  
pp. 4537-4549 ◽  
Author(s):  
Andreas Orthaber ◽  
Michael Karnahl ◽  
Stefanie Tschierlei ◽  
Daniel Streich ◽  
Matthias Stein ◽  
...  
Keyword(s):  
Electronic Properties ◽  
Active Site ◽  
Iron Complexes ◽  
Computational Studies ◽  
Mononuclear Iron ◽  
Conformational Isomers ◽  
Ligand Modification ◽  
Fe Complexes ◽  
Ir Spectroscopic

6 Fe complexes of the type [Fe(X-bdt)(PR2NPh2)(CO)] were prepared and the possibility to tune their electronic properties by ligand modification was demonstrated. IR spectroscopic and computational studies suggest that the compounds exist as a mixture of isomers in solution.

scholarly journals A 2‐Tyr‐1‐carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase

2020 ◽  
Vol 132 (39) ◽  
pp. 17109-17114
Author(s):  
Chetan Kumar Arya ◽  
Swati Yadav ◽  
Jonathan Fine ◽  
Ana Casanal ◽  
Gaurav Chopra ◽  
...  
Keyword(s):  
Active Site ◽  
Mononuclear Iron ◽  
Iron Center

scholarly journals A 2‐Tyr‐1‐carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase

2020 ◽  
Vol 59 (39) ◽  
pp. 16961-16966
Author(s):  
Chetan Kumar Arya ◽  
Swati Yadav ◽  
Jonathan Fine ◽  
Ana Casanal ◽  
Gaurav Chopra ◽  
...  
Keyword(s):  
Active Site ◽  
Mononuclear Iron ◽  
Iron Center

Aerobic catabolism of sterols by microorganisms: key enzymes that open the 3-ketosteroid nucleus

2019 ◽  
Vol 366 (14) ◽  
Author(s):  
Joseph Kreit
Keyword(s):  
Active Site ◽  
Published Data ◽  
Aerobic Degradation ◽  
Key Enzymes ◽  
Mononuclear Iron ◽  
Catalytic Unit

ABSTRACT Aerobic degradation of the sterol tetracyclic nucleus by microorganisms comprises the catabolism of A/B-rings, followed by that of C/D-rings. B-ring rupture at the C9,10-position is a key step involving 3-ketosteroid Δ1-dehydrogenase (KstD) and 3-ketosteroid 9α-hydroxylase (KstH). Their activities lead to the aromatization of C4,5-en-containing A-ring causing the rupture of B-ring. C4,5α-hydrogenated 3-ketosteroid could be produced by the growing microorganism containing a 5α-reductase. In this case, the microorganism synthesizes, in addition to KstD and KstH, a 3-ketosteroid Δ4-(5α)-dehydrogenase (Kst4D) in order to produce the A-ring aromatization, and consequently B-ring rupture. KstD and Kst4D are FAD-dependent oxidoreductases. KstH is composed of a reductase and a monooxygenase. This last component is the catalytic unit; it contains a Rieske-[2Fe-2S] center with a non-haem mononuclear iron in the active site. Published data regarding these enzymes are reviewed.

scholarly journals One enzyme, many reactions: structural basis for the various reactions catalyzed by naphthalene 1,2-dioxygenase

IUCrJ ◽  
2017 ◽  
Vol 4 (5) ◽  
pp. 648-656 ◽  
Author(s):  
Daniel J. Ferraro ◽  
Adam Okerlund ◽  
Eric Brown ◽  
S. Ramaswamy
Keyword(s):  
Active Site ◽  
Binding Pocket ◽  
Nonheme Iron ◽  
Structural Basis ◽  
Mononuclear Iron

Rieske nonheme iron oxygenases (ROs) are a well studied class of enzymes. Naphthalene 1,2-dioxygenase (NDO) is used as a model to study ROs. Previous work has shown how side-on binding of oxygen to the mononuclear iron provides this enzyme with the ability to catalyze stereospecific and regiospecificcis-dihydroxylation reactions. It has been well documented that ROs catalyze a variety of other reactions, including mono-oxygenation, desaturation, O- and N-dealkylation, sulfoxidationetc. NDO itself catalyzes a variety of these reactions. Structures of NDO in complex with a number of different substrates show that the orientation of the substrate in the active site controls not only the regiospecificity and stereospecificity, but also the type of reaction catalyzed. It is proposed that the mononuclear iron-activated dioxygen attacks the atoms of the substrate that are most proximal to it. The promiscuity of delivering two products (apparently by two different reactions) from the same substrate can be explained by the possible binding of the substrate in slightly different orientations aided by the observed flexibility of residues in the binding pocket.

Mononuclear Iron(II) Dicarbonyls Derived from NNS Ligands - Structural Models Related to a “Pre-Acyl” Active Site of Mono-Iron (Hmd) Hydrogenase

2015 ◽  
Vol 2015 (10) ◽  
pp. 1675-1691 ◽  
Author(s):  
Keren A. Thomas Muthiah ◽  
Gummadi Durgaprasad ◽  
Zhu-Lin Xie ◽  
Owen M. Williams ◽  
Christopher Joseph ◽  
...  
Keyword(s):  
Active Site ◽  
Structural Models ◽  
Mononuclear Iron

scholarly journals A mononuclear iron carbonyl complex [Fe(μ-bdt)(CO)2(PTA)2] with bulky phosphine ligands: a model for the [FeFe] hydrogenase enzyme active site with an inverted redox potential

2017 ◽  
Vol 46 (30) ◽  
pp. 10050-10056 ◽  
Author(s):  
M. Natarajan ◽  
H. Faujdar ◽  
S. M. Mobin ◽  
M. Stein ◽  
S. Kaur-Ghumaan
Keyword(s):  
Redox Potential ◽  
Hydrogen Evolution ◽  
Active Site ◽  
Acidic Solution ◽  
Iron Complex ◽  
Phosphine Ligands ◽  
Carbonyl Complex ◽  
Enzyme Active Site ◽  
Mononuclear Iron ◽  
Hydrogenase Enzyme

This mononuclear iron complex displays an inverted redox potential and catalyzes hydrogen evolution in acidic solution.

scholarly journals Breaking a Strong Amide Bond: Structure and Properties of Dimethylformamidase

2019 ◽  
Author(s):  
Chetan Kumar Arya ◽  
Swati Yadav ◽  
Jonathan Fine ◽  
Ana Casanal ◽  
Gaurav Chopra ◽  
...  
Keyword(s):  
Nitrogen Source ◽  
Active Site ◽  
Active Sites ◽  
Bacterial Species ◽  
Amide Bond ◽  
Dimethyl Formamide ◽  
Hydrolytic Cleavage ◽  
Oligomeric State ◽  
Carbon And Nitrogen ◽  
Mononuclear Iron

AbstractDimethylformamidase (DMFase) breaks down the human-made synthetic solvent N,N-dimethyl formamide(DMF) used extensively in industry(1). DMF is not known to exist in nature and was first synthesized in 1893. In spite of the recent origin of DMF, certain bacterial species such as Paracoccus, Pseudomonas, and Alcaligenes have evolved pathways to breakdown DMF and use them as carbon and nitrogen source for growth(2, 3). The work presented here provides a molecular basis for the ability of DMFase from Paracoccus to function in exacting conditions of high solvent concentrations, temperature and ionic strength to catalyze the hydrolysis of a stable amide bond. The structure reveals a multimeric complex of the α2β2 type or (α2β2)2 type. One of the three domains of the large subunit and the small subunit are hitherto undescribed folds and as yet of unknown evolutionary origin. The active site is made of a distinctive mononuclear iron that is coordinated by two tyrosine residues and a glutamic acid residue. The hydrolytic cleavage of the amide bond is catalyzed at the Fe3+ site with a proximal glutamate probably acting as the base. The change in the quaternary structure is salt dependent with high salt resulting in the larger oligomeric state. Kinetic characterization reveals an enzyme that shows cooperativity between subunits and the structure provides clues on the interconnection between the active sites.Significance StatementN,N-dimethyl formamide(DMF) is a commonly used industrial solvent that was first synthesized in 1893. The properties that make DMF a highly desired solvent also makes it a difficult compound to breakdown. Yet, certain bacteria have evolved to survive in environments polluted by DMF and have enzymes that breakdown DMF and use it as their carbon and nitrogen source. The molecular structure of the enzyme that breaks down the stable amide bond in these bacteria, reveals two new protein folds and a unique mononuclear iron active site. The work reported here provides the structural and biochemical framework to query the evolutionary origins of the protein, as well as in engineering this enzyme for use in bioremediation of a human made toxic solvent.

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