3VM1

assimilatory nitrite reductase (Nii3) - N226K mutant - HCO3 complex from tobacco leaf

Summary for 3VM1

• Entry DOI: 10.2210/pdb3vm1/pdb
• Related: 3B0G 3VLX 3VLY 3VLZ 3VM0
• Descriptor: Nitrite reductase, SIROHEME, IRON/SULFUR CLUSTER, ... (7 entities in total)
• Functional Keywords: nii3 n226k mutant, hco3 complex, 3 alpha/beta domains, reductase, oxidoreductase
• Biological source: Nicotiana tabacum (tobacco)
• Total number of polymer chains: 1
• Total formula weight: 67025.45

Authors

Nakano, S.,Takahashi, M.,Sakamoto, A.,Morikawa, H.,Katayanagi, K. (deposition date: 2011-12-05, release date: 2012-09-26, Last modification date: 2023-12-27)

Primary citation

Nakano, S.,Takahashi, M.,Sakamoto, A.,Morikawa, H.,Katayanagi, K.
X-ray crystal structure of a mutant assimilatory nitrite reductase that shows sulfite reductase-like activity
Chem.Biodivers., 9:1989-1999, 2012

PubMed Abstract: Assimilatory nitrite reductase (aNiR) reduces nitrite ions (NO(2)(-)) to ammonium ions (NH(4)(+)), whereas assimilatory sulfite reductase reduces sulfite (SO(3)(2-)) to hydrogen sulfide (HS(-)). Although aNiR can also reduce SO(3)(2-), its activity is much lower than when NO(2)(-) is reduced as the substrate. To increase the SO(3)(2-)-reduction activity of aNiR, we performed a N226K mutation of Nii3, a representative aNiR. The resulting Nii3-N226K variant could bind non-native targets, SO(3)(2-), and HCO(3)(-), in addition to its native target, i.e., NO(2)(-). We have determined the high-resolution structure of Nii3-N226K in its apo-state and in complex with SO(3)(2-), NO(2)(-), and HCO(3)(-). This analysis revealed conformational changes of Lys226 and the adjacent Lys224 upon binding of SO(3)(2-), but not NO(2)(-)In contrast, HCO(3)(-) binding induced a conformational change at Arg179. After replacing Asn226 with a positively charged Lys, aNiR showed affinity for several anions. A comparison of all ligand-bound structures for Nii3-N226K revealed that structural changes in the active site depend on the size of the substrate.

PubMed: 22976986
DOI: 10.1002/cbdv.201100442

Experimental method

X-RAY DIFFRACTION (1.5 Å)