3WVD

Crystal structure of Nitrile Hydratase mutant bR56K complexed with Trimethylacetonitrile, photo-activated for 50 min

Summary for 3WVD

• Entry DOI: 10.2210/pdb3wvd/pdb
• Related: 3WVE
• Descriptor: Nitrile hydratase subunit alpha, Nitrile hydratase subunit beta, FE (III) ION, ... (6 entities in total)
• Functional Keywords: cysteine sulfinic acid, cys-so2h, cys-soh, lyase
• Biological source: Rhodococcus erythropolis; More
• Total number of polymer chains: 2
• Total formula weight: 46763.25

Authors

Yamanaka, Y.,Hashimoto, K.,Noguchi, K.,Yohda, M.,Odaka, M. (deposition date: 2014-05-17, release date: 2015-06-17, Last modification date: 2024-10-30)

Primary citation

Yamanaka, Y.,Kato, Y.,Hashimoto, K.,Iida, K.,Nagasawa, K.,Nakayama, H.,Dohmae, N.,Noguchi, K.,Noguchi, T.,Yohda, M.,Odaka, M.
Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile.
Angew.Chem.Int.Ed.Engl., 54:10763-10767, 2015

PubMed Abstract: The reaction mechanism of nitrile hydratase (NHase) was investigated using time-resolved crystallography of the mutant NHase, in which βArg56, strictly conserved and hydrogen bonded to the two post-translationally oxidized cysteine ligands, was replaced by lysine, and pivalonitrile was the substrate. The crystal structures of the reaction intermediates were determined at high resolution (1.2-1.3 Å). In combination with FTIR analyses of NHase following hydration in H2 (18) O, we propose that the metal-coordinated substrate is nucleophilically attacked by the O(SO(-) ) atom of αCys114-SO(-) , followed by nucleophilic attack of the S(SO(-) ) atom by a βArg56-activated water molecule to release the product amide and regenerate αCys114-SO(-) .

PubMed: 26333053
DOI: 10.1002/anie.201502731

Experimental method

X-RAY DIFFRACTION (1.18 Å)