Structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.01 A resolution

Experimental Data Snapshot

  • Resolution: 1.01 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.109 
  • R-Value Observed: 0.110 

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Structures of protein-protein complexes involved in electron transfer.

Antonyuk, S.V.Han, C.Eady, R.R.Hasnain, S.S.

(2013) Nature 496: 123-126

  • DOI: https://doi.org/10.1038/nature11996
  • Primary Citation of Related Structures:  
    2YQB, 3ZBM, 3ZIY, 4AX3

  • PubMed Abstract: 

    Electron transfer reactions are essential for life because they underpin oxidative phosphorylation and photosynthesis, processes leading to the generation of ATP, and are involved in many reactions of intermediary metabolism. Key to these roles is the formation of transient inter-protein electron transfer complexes. The structural basis for the control of specificity between partner proteins is lacking because these weak transient complexes have remained largely intractable for crystallographic studies. Inter-protein electron transfer processes are central to all of the key steps of denitrification, an alternative form of respiration in which bacteria reduce nitrate or nitrite to N2 through the gaseous intermediates nitric oxide (NO) and nitrous oxide (N2O) when oxygen concentrations are limiting. The one-electron reduction of nitrite to NO, a precursor to N2O, is performed by either a haem- or copper-containing nitrite reductase (CuNiR) where they receive an electron from redox partner proteins a cupredoxin or a c-type cytochrome. Here we report the structures of the newly characterized three-domain haem-c-Cu nitrite reductase from Ralstonia pickettii (RpNiR) at 1.01 Å resolution and its M92A and P93A mutants. Very high resolution provides the first view of the atomic detail of the interface between the core trimeric cupredoxin structure of CuNiR and the tethered cytochrome c domain that allows the enzyme to function as an effective self-electron transfer system where the donor and acceptor proteins are fused together by genomic acquisition for functional advantage. Comparison of RpNiR with the binary complex of a CuNiR with a donor protein, AxNiR-cytc551 (ref. 6), and mutagenesis studies provide direct evidence for the importance of a hydrogen-bonded water at the interface in electron transfer. The structure also provides an explanation for the preferential binding of nitrite to the reduced copper ion at the active site in RpNiR, in contrast to other CuNiRs where reductive inactivation occurs, preventing substrate binding.

  • Organizational Affiliation

    Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COPPER-CONTAINING NITRITE REDUCTASE468Ralstonia pickettii 12JMutation(s): 0 
Find proteins for B2UHR8 (Ralstonia pickettii (strain 12J))
Explore B2UHR8 
Go to UniProtKB:  B2UHR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2UHR8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.01 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.109 
  • R-Value Observed: 0.110 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.177α = 90
b = 128.177β = 90
c = 86.314γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Database references
  • Version 2.0: 2019-01-23
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description