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

DOI: 10.1107/S2052252517007527 DOI Help

Authors: Kakali Sen (University of Essex; STFC Daresbury Laboratory) , Sam Horrell (University of Essex) , Demet Kekilli (University of Essex) , Chin W. Yong (STFC Daresbury Laboratory) , Thomas W. Keal (STFC Daresbury Laboratory) , Hakan Atakisi (Cornell University) , David W. Moreau (Cornell University) , Robert E. Thorne (Cornell University) , Michael A. Hough (University of Essex) , Richard W. Strange (STFC Daresbury Laboratory)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Iucrj , VOL 4

State: Published (Approved)
Published: July 2017
Diamond Proposal Number(s): 13467

Open Access Open Access

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 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.

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

Subject Areas: Biology and Bio-materials

Instruments: I02-Macromolecular Crystallography

Other Facilities: Cornell High Energy Synchrotron Source (CHESS)


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