2AKJ

Structure of spinach nitrite reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Spinach Nitrite Reductase: Implications for Multi-electron Reactions by the Iron-Sulfur:Siroheme Cofactor

Swamy, U.Wang, M.Tripathy, J.N.Kim, S.K.Hirasawa, M.Knaff, D.B.Allen, J.P.

(2005) Biochemistry 44: 16054-16063

  • DOI: 10.1021/bi050981y

  • PubMed Abstract: 
  • The structure of nitrite reductase, a key enzyme in the process of nitrogen assimilation, has been determined using X-ray diffraction to a resolution limit of 2.8 A. The protein has a globular fold consisting of 3 alpha/beta domains with the siroheme ...

    The structure of nitrite reductase, a key enzyme in the process of nitrogen assimilation, has been determined using X-ray diffraction to a resolution limit of 2.8 A. The protein has a globular fold consisting of 3 alpha/beta domains with the siroheme-iron sulfur cofactor at the interface of the three domains. The Fe(4)S(4) cluster is coordinated by cysteines 441, 447, 482, and 486. The siroheme is located at a distance of 4.2 A from the cluster, and the central iron atom is coordinated to Cys 486. The siroheme is surrounded by several ionizable amino acid residues that facilitate the binding and subsequent reduction of nitrite. A model for the ferredoxin:nitrite reductase complex is proposed in which the binding of ferredoxin to a positively charged region of nitrite reductase results in elimination of exposure of the cofactors to the solvent. The structure of nitrite reductase shows a broad similarity to the hemoprotein subunit of sulfite reductase but has many significant differences in the backbone positions that could reflect sequence differences or could arise from alterations of the sulfite reductase structure that arise from the isolation of this subunit from the native complex. The implications of the nitrite reductase structure for understanding multi-electron processes are discussed in terms of differences in the protein environments of the cofactors.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Arizona State University, Tempe Arizona 85287-1604, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferredoxin--nitrite reductase, chloroplast
A
608Spinacia oleraceaMutation(s): 0 
Gene Names: NIR
EC: 1.7.7.1
Find proteins for P05314 (Spinacia oleracea)
Go to UniProtKB:  P05314
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SRM
Query on SRM

Download SDF File 
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: 2.8 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.250 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.970α = 90.00
b = 128.970β = 90.00
c = 120.950γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata reduction
d*TREKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection