4OB3

Crystal Structure of Nitrile Hydratase from Pseudonocardia thermophila : A Reference Structure to Boronic Acid Inhibition of Nitrile Hydratase

Summary for 4OB3

• Entry DOI: 10.2210/pdb4ob3/pdb
• Related: 4OB0 4OB1 4OB2
• Descriptor: Cobalt-containing nitrile hydratase subunit alpha, Cobalt-containing nitrile hydratase subunit beta, COBALT (II) ION, ... (5 entities in total)
• Functional Keywords: nitrile hydratase, nulceophile, lyase
• Biological source: Pseudonocardia thermophila; More
• Total number of polymer chains: 2
• Total formula weight: 50854.22

Authors

Rui, W.,Salette, M.,Ruslan, S.,Richard, H.,Dali, L. (deposition date: 2014-01-06, release date: 2014-11-26, Last modification date: 2024-10-30)

Primary citation

Martinez, S.,Wu, R.,Sanishvili, R.,Liu, D.,Holz, R.
The active site sulfenic acid ligand in nitrile hydratases can function as a nucleophile.
J.Am.Chem.Soc., 136:1186-1189, 2014

PubMed Abstract: Nitrile hydratase (NHase) catalyzes the hydration of nitriles to their corresponding commercially valuable amides at ambient temperatures and physiological pH. Several reaction mechanisms have been proposed for NHase enzymes; however, the source of the nucleophile remains a mystery. Boronic acids have been shown to be potent inhibitors of numerous hydrolytic enzymes due to the open shell of boron, which allows it to expand from a trigonal planar (sp(2)) form to a tetrahedral form (sp(3)). Therefore, we examined the inhibition of the Co-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) by boronic acids via kinetics and X-ray crystallography. Both 1-butaneboronic acid (BuBA) and phenylboronic acid (PBA) function as potent competitive inhibitors of PtNHase. X-ray crystal structures for BuBA and PBA complexed to PtNHase were solved and refined at 1.5, 1.6, and 1.2 Å resolution. The resulting PtNHase-boronic acid complexes represent a "snapshot" of reaction intermediates and implicate the cysteine-sulfenic acid ligand as the catalytic nucleophile, a heretofore unknown role for the αCys(113)-OH sulfenic acid ligand. Based on these data, a new mechanism of action for the hydration of nitriles by NHase is presented.

PubMed: 24383915
DOI: 10.1021/ja410462j

Experimental method

X-RAY DIFFRACTION (1.92 Å)