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

IUCrJ

Hakan Atakisi¹  Robert E. Thorne¹  David W. Moreau¹  Sam Horrell²  Michael A. Hough²  Richard W. Strange²  Kakali Sen²  Demet Kekilli²  Thomas W. Keal³  Chin W. Yong³ 

[1] Physics Department, Cornell University, Ithaca, NY 14853, USA;School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England;Scientific Computing Department, STFC Daresbury Laboratory, Warrington WA4 4AD, England;

关键词: serial crystallography;    high temperature;    catalysis;    molecular dynamics;    density functional theory;    denitrification;    copper nitrite reductase;    radiolysis;    synchrotron radiation;   

DOI  :  10.1107/S2052252517007527

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown