5N8H

Serial Cu nitrite reductase structures at elevated cryogenic temperature, 240K. Dataset 3.

Summary for 5N8H

• Entry DOI: 10.2210/pdb5n8h/pdb
• Descriptor: Copper-containing nitrite reductase, COPPER (II) ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: nitrite reductase, copper enzyme, trimer, cupredoxid domain, oxidoreductase
• Biological source: Achromobacter cycloclastes
• Cellular location: Periplasm: P25006
• Total number of polymer chains: 1
• Total formula weight: 37324.80

Authors

Horrell, S.,Kekilli, D.,Hough, M.,Strange, R. (deposition date: 2017-02-23, release date: 2017-07-26, Last modification date: 2024-01-17)

Primary citation

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.
Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase.
IUCrJ, 4:495-505, 2017

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 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 and His) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the Asp protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site 'capping residue' (Ile), a determinant of ligand binding, are influenced both by temperature and by the protonation state of Asp. A previously unobserved conformation of Ile 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.

PubMed: 28875036
DOI: 10.1107/S2052252517007527

Experimental method

X-RAY DIFFRACTION (1.65 Å)