3VLX

Assimilatory nitrite reductase (Nii3) - N226K mutant - ligand free form from tobacco leaf


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

X-ray crystal structure of a mutant assimilatory nitrite reductase that shows sulfite reductase-like activity

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

(2012) Chem Biodivers 9: 1989-1999

  • DOI: https://doi.org/10.1002/cbdv.201100442
  • Primary Citation of Related Structures:  
    3VLX, 3VLY, 3VLZ, 3VM0, 3VM1

  • 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.


  • Organizational Affiliation

    Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima 739-8526, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrite reductase584Nicotiana tabacumMutation(s): 1 
Gene Names: nii3
EC: 1.7.7.1
UniProt
Find proteins for Q76KB0 (Nicotiana tabacum)
Explore Q76KB0 
Go to UniProtKB:  Q76KB0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ76KB0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SRM
Query on SRM

Download Ideal Coordinates CCD File 
B [auth A]SIROHEME
C42 H44 Fe N4 O16
DLKSSIHHLYNIKN-MWBYXLBFSA-L
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.498α = 90
b = 133.498β = 90
c = 77.77γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-12-27
    Changes: Data collection, Non-polymer description, Structure summary