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

作者：Sen Kakali; Horrell Sam; Kekilli Demet; Yong Chin W; Keal Thomas W; Atakisi Hakan; Moreau David W; Thorne Robert E; Hough Michael A; Strange Richard W^*

来源：IUCrJ, 2017, 4(4): 495-505.

DOI：10.1107/S2052252517007527

• serial crystallography
• high temperature
• catalysis
• molecular dynamics
• density functional theory
• denitrification
• copper nitrite reductase
• radiolysis
• synchrotron radiation

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 AspCAT 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.

• 出版日期2017-7