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Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase

Sen, K and Horrell, S and Kekilli, D and Yong, CW and Keal, TW and Atakisi, H and Moreau, DW and Thorne, RE and Hough, MA and Strange, RW (2017) 'Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase.' IUCrJ, 4. 495 - 505. ISSN 2052-2525

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Abstract

© Kakali Sen et al. 2017. Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (Asp CAT and His CAT) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the Asp CAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site 'capping residue' (Ile CAT), a determinant of ligand binding, are influenced both by temperature and by the protonation state of Asp CAT. A previously unobserved conformation of Ile CAT is seen in the elevated temperature series compared with 100K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.

Item Type: Article
Subjects: Q Science > QD Chemistry
Divisions: Faculty of Science and Health > Biological Sciences, School of
Depositing User: Mike Hough
Date Deposited: 26 Jun 2017 15:03
Last Modified: 04 Feb 2019 12:15
URI: http://repository.essex.ac.uk/id/eprint/19966

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