Breaking a Strong Amide Bond: Structure and Properties of Dimethylformamidase

Abstract

Dimethylformamidase (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 like Paracoccus, Pseudomonas, and Alcaligenes have evolved pathways to breakdown DMF and use them as carbon and nitrogen source for growth(2, 3). The structure of DMFase from Paracoccus and the biochemical studies reported here provide a molecular basis for its stability, substrate specificity and catalysis. The structure reveals a multimeric complex of the a2b2 type or (a2b2)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 Fe 3+ 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. KRV thanks SERB, India for the Ramanujan Fellowship. GC acknowledges start-up funds from Contributions: RG and RS conceived the project. RG, RS and KRV designed the experiments. SY, AC and KRV carried out sample preparation, EM data collection analysis. KRV built the initial model. CA and RS carried out the X-ray structure determination and analysis. CA carried out most of the biochemical studies. JF and GC carried out the DFT calculations. CA, RS, RG, GC and KRV wrote the manuscript. All authors reviewed and made corrections to the manuscript.

Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures

“…4). The small subunit is likely to play a role in structural stabilization of the large subunit (Arya et al 2020), but it is unclear why the small subunit is only present in certain genera. Averaged from all the enriched microbial communities in the treatments with BTEX, dominant genera (i.e., Pseudomonas, Rhodococcus, Achromobacter, Alicycliphilus, and Comamonas) generally carry relative highly abundant genes involved in the degradation of BTEX (Fig.…”