Sunday, September 27, 2015

Nitrite binding modes in CuNIR

Fukuda and Inoue [1] have determined the crystal structure of the C135A mutant of thermostable copper nitrite reductase (CuNIR) from Geobacillus thermodenitrificans in complex with nitrite to 1.55 Å resolution. Interestingly, this high-temperature (320 K) structure [2] displays a near-bidentate binding mode of nitrite distinct from a monodentate mode in a cryogenic structure [3]:

To our knowledge, this is the first case in which the difference in substrate binding modes between cryogenic and high-temperature structures has been visualized by crystallography.
The copper site geometries are given in Table 1.

Table 1 (adapted from [4])

Cu—Ligand Distances (Å) 3X1N (320 K) 3WKP (100 K)
I. Type 1 Cu—residue distances
T1Cu—H95Nδ1 2.08 2.14
T1Cu—H143Nδ1 2.01 1.96
T1Cu—M148Sδ 2.13 2.07
II. Type 2 Cu—residue distances
T2Cu—H100Nε2 2.07 1.96
T2Cu—H134Nε2 2.00 1.95
T2Cu—H294Nε2 1.98 2.01
T2Cu—water 2.02 n/a
III. Type 2 Cu—nitrite distances
T2Cu—Oproximal 2.13 1.97
T2Cu—N 2.21 2.85
T2Cu—Odistal 2.52 3.41
  1. Fukuda, Y. and Inoue, T. (2015) High-temperature and high-resolution crystallography of thermostable copper nitrite reductase. Chemical Communications 51, 6532—6535.
  2. PDB:3X1N
  3. PDB:3WKP
  4. Fukuda, Y. and Inoue, T. (2015) High-temperature and high-resolution crystallography of thermostable copper nitrite reductase. Electronic Supplementary Material.