2ZPH

Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 340min at 293K

Summary for 2ZPH

• Entry DOI: 10.2210/pdb2zph/pdb
• Related: 2AHJ 2CZ6 2CZ7 2D0Q 2ZPB 2ZPE 2ZPF 2ZPG 2ZPI
• Descriptor: Nitrile hydratase subunit alpha, Nitrile hydratase subunit beta, FE (III) ION, ... (7 entities in total)
• Functional Keywords: lyase, iron, metal-binding, oxidation
• Biological source: Rhodococcus erythropolis; More
• Total number of polymer chains: 2
• Total formula weight: 46782.21

Authors

Hashimoto, K.,Suzuki, H.,Taniguchi, K.,Noguchi, T.,Yohda, M.,Odaka, M. (deposition date: 2008-07-11, release date: 2008-10-21, Last modification date: 2024-10-09)

Primary citation

Hashimoto, K.,Suzuki, H.,Taniguchi, K.,Noguchi, T.,Yohda, M.,Odaka, M.
Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crystallography using a novel substrate, tert-butylisonitrile
J.Biol.Chem., 283:36617-36623, 2008

PubMed Abstract: Nitrile hydratases (NHases) have an unusual iron or cobalt catalytic center with two oxidized cysteine ligands, cysteine-sulfinic acid and cysteine-sulfenic acid, catalyzing the hydration of nitriles to amides. Recently, we found that the NHase of Rhodococcus erythropolis N771 exhibited an additional catalytic activity, converting tert-butylisonitrile (tBuNC) to tert-butylamine. Taking advantage of the slow reactivity of tBuNC and the photoreactivity of nitrosylated NHase, we present the first structural evidence for the catalytic mechanism of NHase with time-resolved x-ray crystallography. By monitoring the reaction with attenuated total reflectance-Fourier transform infrared spectroscopy, the product from the isonitrile carbon was identified as a CO molecule. Crystals of nitrosylated inactive NHase were soaked with tBuNC. The catalytic reaction was initiated by photo-induced denitrosylation and stopped by flash cooling. tBuNC was first trapped at the hydrophobic pocket above the iron center and then coordinated to the iron ion at 120 min. At 440 min, the electron density of tBuNC was significantly altered, and a new electron density was observed near the isonitrile carbon as well as the sulfenate oxygen of alphaCys114. These results demonstrate that the substrate was coordinated to the iron and then attacked by a solvent molecule activated by alphaCys114-SOH.

PubMed: 18948265
DOI: 10.1074/jbc.M806577200

Experimental method

X-RAY DIFFRACTION (1.59 Å)