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Cofactor assisted gating mechanism in the active site of NADH oxidase from Thermus thermophilus by Jozef Hritz; Gabriel Žoldák; Erik Sedlák is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

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## Abstract NADH oxidase (NOX) from __Thermus thermophilus__ is a member of a structurally homologous flavoprotein family of nitroreductases and flavin reductases. The importance of local conformational dynamics in the active site of NOX has been recently demonstrated. The enzyme activity was increased by 250% in the presence of 1 M urea with no apparent perturbation of the native structure of the protein. The present __in silico__ results correlate with the __in vitro__ data and suggest the possible explanation about the effect of urea on NOX activity at the molecular level. Both, X‐ray structure and molecular dynamics (MD) simulations, show open conformation of the active site represented by −f0.9 nm distance between the indole ring of Trp47 and the isoalloxazine ring of FMN412. In this conformation, the substrate molecule can bind in the active site without sterical restraints. MD simulations also indicate more stable conformation of the active site called “closed” conformation. In this conformation, Trp47 and the isoalloxazine ring of FMN412 are so close to each other (−f0.5 nm) that the substrate molecule is unable to bind between them without perturbing this conformation. The

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Author

Jozef Hritz; Gabriel Žoldák; Erik Sedlák

Publisher

John Wiley and Sons; Wiley (John Wiley & Sons); Wiley-Liss Inc; Wiley (ISSN 0887-3585)

Published

2006

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)