Structure of spinach nitrite reductase

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

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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: https://doi.org/10.1021/bi050981y
  • Primary Citation of Related Structures:  

  • 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-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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin--nitrite reductase, chloroplast608Spinacia oleraceaMutation(s): 0 
Gene Names: NIR
Find proteins for P05314 (Spinacia oleracea)
Explore P05314 
Go to UniProtKB:  P05314
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05314
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SRM

Download Ideal Coordinates CCD File 
C42 H44 Fe N4 O16
Query on SF4

Download Ideal Coordinates CCD File 
Fe4 S4
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.97α = 90
b = 128.97β = 90
c = 120.95γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
CrystalCleardata reduction
d*TREKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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