PDBsum entry 3vkt

Oxidoreductase

PDB id: 3vkt

Contents

Protein chain

538 a.a.

Ligands

SRM

SF4

HOA

Metals

__K

_CL ×2

Waters ×1060

PDB id:

3vkt

Name:

Oxidoreductase

Title:

Assimilatory nitrite reductase (nii3) - nh2oh complex from tobbaco leaf

Structure:

Nitrite reductase. Chain: a. Fragment: unp residues 19-587. Synonym: nii3. Engineered: yes

Source:

Nicotiana tabacum. Tobacco. Organism_taxid: 4097. Gene: nii3. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.30Å R-factor: 0.155 R-free: 0.164

Authors:

S.Nakano,M.Takahashi,A.Sakamoto,H.Morikawa,K.Katayanagi

Key ref:

S.Nakano et al. (2012). The reductive reaction mechanism of tobacco nitrite reductase derived from a combination of crystal structures and ultraviolet-visible microspectroscopy. Proteins, 80, 2035-2045. PubMed id: 22499059

Date:

20-Nov-11 Release date: 25-Apr-12

Protein chain

Q76KB0  (Q76KB0_TOBAC) -  Nitrite reductase from Nicotiana tabacum

Seq: 587 a.a.

Struc: 538 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.7.7.1 - ferredoxin--nitrite reductase.
• Reaction: 6 oxidized [2Fe-2S]-[ferredoxin] + NH4⁺ + 2 H2O = nitrite + 6 reduced [2Fe-2S]-[ferredoxin] + 8 H⁺

6 × oxidized [2Fe-2S]-[ferredoxin] + NH4(+) + 2 × H2O = nitrite + 6 × reduced [2Fe-2S]-[ferredoxin] (Bound ligand (Het Group name = HOA) matches with 66.67% similarity) + 8 × H(+)

• Cofactor: Iron-sulfur; Siroheme

Iron-sulfur Siroheme (Bound ligand (Het Group name = SRM) matches with 96.88% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Proteins 80:2035-2045 (2012)

PubMed id: 22499059

The reductive reaction mechanism of tobacco nitrite reductase derived from a combination of crystal structures and ultraviolet-visible microspectroscopy.

S.Nakano, M.Takahashi, A.Sakamoto, H.Morikawa, K.Katayanagi.

ABSTRACT

Assimilatory nitrite reductase (aNiR) reduces nitrite to an ammonium ion and has siroheme and a [Fe(4)S(4)] cluster as prosthetic groups. A reaction mechanism for Nii3, an aNiR from tobacco, is proposed based on high resolution X-ray structures and UV-Vis (ultraviolet-visible) microspectroscopy of Nii3-ligand complexes. Analysis of UV-Vis spectral changes in Nii3 crystals with increasing X-ray exposure showed prosthetic group reductions. In Nii3-NO2(-) structures, X-ray irradiation enhanced the progress of the reduction reaction, and cleavage of the N-O bond was observed when X-ray doses were increased. Crystal structures of Nii3 with other bound ligands, such as Nii3-NO and Nii3-NH(2)OH, were also determined. Further, by combining information from these Nii3 ligand-bound structures, including that of Nii3-NO2(-), with UV-Vis microspectral data obtained using different X-ray doses, a reaction mechanism for aNiR was suggested. Cleavage of the two N-O bonds of nitrite was envisaged as a two-step process: first, the N-O bond close to Lys224 was cleaved, followed by cleavage of the N-O bond close to Arg109. X-ray structures also indicated that aNiR-catalyzed nitrite reduction proceeded without the need for conformation changes in active site residues. Geometrical changes in the ligand molecules and the placement of neighboring water molecules appeared to be important to the stability of the active site residue interactions (Arg109, Arg179, and Lys224) and the ligand molecule. These interactions may contribute to the efficiency of aNiR reduction reactions.