Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase.Sen, K., Horrell, S., Kekilli, D., Yong, C.W., Keal, T.W., Atakisi, H., Moreau, D.W., Thorne, R.E., Hough, M.A., Strange, R.W.
(2017) IUCrJ 4: 495-505
- PubMed: 28875036
- DOI: 10.1107/S2052252517007527
- Primary Citation of Related Structures:
5N8H, 5N8G, 5N8I, 5N8F
- PubMed Abstract:
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 simulation ...
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 (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 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.
School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England.