Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase
| Autor: | Kakali Sen, Sam Horrell, Demet Kekilli, Chin W. Yong, Thomas W. Keal, Hakan Atakisi, David W. Moreau, Robert E. Thorne, Michael A. Hough, Richard W. Strange |
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| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: | |
| Zdroj: | IUCrJ, Vol 4, Iss 4, Pp 495-505 (2017) |
| Druh dokumentu: | article |
| ISSN: | 2052-2525 20522525 |
| DOI: | 10.1107/S2052252517007527 |
| Popis: | 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 240 K, 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 (AspCAT and HisCAT) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the AspCAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site `capping residue' (IleCAT), a determinant of ligand binding, are influenced both by temperature and by the protonation state of AspCAT. A previously unobserved conformation of IleCAT is seen in the elevated temperature series compared with 100 K 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. |
| Databáze: | Directory of Open Access Journals |
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