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


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.

SUBMITTER: Sen K 

PROVIDER: S-EPMC5571812 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Active-site protein dynamics and solvent accessibility in native <i>Achromobacter cycloclastes</i> copper nitrite reductase.

Sen Kakali K   Horrell Sam S   Kekilli Demet D   Yong Chin W CW   Keal Thomas W TW   Atakisi Hakan H   Moreau David W DW   Thorne Robert E RE   Hough Michael A MA   Strange Richard W RW  

IUCrJ 20170616 Pt 4


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  ...[more]

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