3B0G

Assimilatory nitrite reductase (Nii3) from tobbaco leaf

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Structure-function relationship of assimilatory nitrite reductases from the leaf and root of tobacco based on high resolution structures

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

(2012) Protein Sci. 21: 383-395

  • DOI: 10.1002/pro.2025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Tobacco expresses four isomers of assimilatory nitrite reductase (aNiR), leaf-type (Nii1 and Nii3), and root-type (Nii2 and Nii4). The high-resolution crystal structures of Nii3 and Nii4, determined at 1.25 and 2.3 Å resolutions, respectively, reveal ...

    Tobacco expresses four isomers of assimilatory nitrite reductase (aNiR), leaf-type (Nii1 and Nii3), and root-type (Nii2 and Nii4). The high-resolution crystal structures of Nii3 and Nii4, determined at 1.25 and 2.3 Å resolutions, respectively, revealed that both proteins had very similar structures. The Nii3 structure provided detailed geometries for the [4Fe-4S] cluster and the siroheme prosthetic groups. We have generated two types of Nii3 variants: one set focuses on residue Met175 (Nii3-M175G, Nii3-M175E, and Nii3-M175K), a residue that is located on the substrate entrance pathway; the second set targets residue Gln448 (Nii3-Q448K), a residue near the prosthetic groups. Comparison of the structures and kinetics of the Nii3 wild-type (Nii3-WT) and the Met175 variants showed that the hydrophobic side-chain of Met175 facilitated enzyme efficiency (k(cat) /K(m) ). The Nii4-WT has Lys449 at the equivalent position of Gln448 in Nii3-WT. The enzyme activity assay revealed that the turnover number (k(cat) ) and Michaelis constant (K(m) ) of Nii4-WT were lower than those of Nii3-WT. However, the k(cat) /K(m) of Nii4-WT was about 1.4 times higher than that of Nii3-WT. A comparison of the kinetics of the Nii3-Q448K and Nii4-K449Q variants revealed that the change in k(cat) /K(m) was brought about by the difference in Residue 448 (defined as Gln448 in Nii3 and Lys449 in Nii4). By combining detailed crystal structures with enzyme kinetics, we have proposed that Nii3 is the low-affinity and Nii4 is the high-affinity aNiR.

    Organizational Affiliation: 

    Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrite reductase
A
591Nicotiana tabacumMutation(s): 0 
Gene Names: nii3
EC: 1.7.7.1
Find proteins for Q76KB0 (Nicotiana tabacum)
Go to UniProtKB:  Q76KB0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4
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Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CL
Query on CL
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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
SRM
Query on SRM
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Download CCD File 
A
SIROHEME
C42 H42 Fe N4 O16
PGYXHNRRBJLFEV-NBUGCWMUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.160 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 134.051α = 90.00
b = 134.051β = 90.00
c = 77.801γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
MOLREPphasing
SCALEPACKdata scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-22
    Type: Initial release