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Monday 7 April 2014

A mechanism model for NHase using a cyclic and a disulfide intermediate.


There is a very interesting paper proposing a new mechanism for the hydration reaction of iron-centred NHases published in Inorganic Chemistry by Kathrin Hopmann. The paper, entitled "Full Reaction Mechanism of Nitrile Hydratase: A Cyclic Intermediate and an Unexpected Disulfide Switch" sides with the opinion that the nitrile ligates to the iron centre. Hopmann suggests that the oxygen of the cysteine post-translationally modified to a sulfenic acid then acts as the nucleophile attached the C-N bond.

 


This oxygen is the one that becomes the oxygen in the nascent amide carbonyl, with the two cysteine sulfurs combining to form a disulfide link.



After loss of the amide from the iron centre, the cysteine is oxidized again using an oxygen from water. My suspicion with all these mechanistic investigation is that it may be that a lot of different mechanisms may operate with the dominant one being very tied to the specific sequence/space properties of each enzyme. I have been a fan of nitrile-bound mechanisms solely on the basis that they seem much more likely to render chiral selectivity which we know is a possibility for some enzymes and some substrates.

I also wonder how the numbers from the calculations reported in this paper change for cobalt centre NHases.

Thursday 3 April 2014

Two publications on the nitrilase from Sphingomonas wittichii RW1


Sphingomonas wittichii RW1 is a bacterium which has been shown to have the ability to degrade polychlorinated dioxins, and hence has had its genome fully sequenced. It has two different nitrilases in its genome.


Two papers just released with the corresponding authors Er-Zheng Su and Dong-Zhi Wei report on the nitrilase with the accession code YP_001264656. These authors and enzyme have previously been mentioned on this blog- I complained there was no information on the enzyme discovery... here it is!

The first entitled “Cloning, Overexpression, andCharacterization of a High Enantioselective Nitrilase from Sphingomonaswittichii RW1 for Asymmetric Synthesis of (R)-Phenylglycine” and published in Applied Biochemistry and Biotechnology: Part A: Enzyme Engineering and Biotechnology describes the construction of a mini-library of nitrilase enzymes chosen by the similarity to a nitrilase from Pseudomonas fluorescens EBC191 (GenBank accession no. AAW79573) which has been shown to be highly activity toward phenylglycinonitrile. The nitrilase from Sphingomonas wittichii RW1 was shown to be most promising nitrilase to achieve chiral synthesis of R-phenylglycine in a kinetic resolution mode.

The second entitled “Efficient asymmetric synthesis ofD-N-formyl-phenylglycine via cross-linked nitrilase aggregates catalyzeddynamic kinetic resolution” and published in Catalysis Communications describes the preparation of cross-linked enzyme aggregates (CLEAs) of nitrilase from Sphingomonas wittichii RW1, and then its use to perform dynamic kinetic resolution to make D-N-formyl-phenylglycine. The paper also demonstrates that the CLEAs have improved stability over non-immobilized enzyme and are reuseable up to six times whilst retaining 70% initial activity.