6THF

Crystal structure of two-domain Cu nitrite reductase from Bradyrhizobium sp. ORS 375


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Reverse protein engineering of a novel 4-domain copper nitrite reductase reveals functional regulation by protein-protein interaction.

Sasaki, D.Watanabe, T.F.Eady, R.R.Garratt, R.C.Antonyuk, S.V.Hasnain, S.S.

(2021) FEBS J 288: 262-280

  • DOI: 10.1111/febs.15324
  • Primary Citation of Related Structures:  
    6THE, 6THF

  • PubMed Abstract: 
  • Cu-containing nitrite reductases that convert NO 2 - to NO are critical enzymes in nitrogen-based energy metabolism. Among organisms in the order Rhizobiales, we have identified two copies of nirK, one encoding a new class of ...

    Cu-containing nitrite reductases that convert NO 2 - to NO are critical enzymes in nitrogen-based energy metabolism. Among organisms in the order Rhizobiales, we have identified two copies of nirK, one encoding a new class of 4-domain CuNiR that has both cytochrome and cupredoxin domains fused at the N terminus and the other, a classical 2-domain CuNiR (Br 2D NiR). We report the first enzymatic studies of a novel 4-domain CuNiR from Bradyrhizobium sp. ORS 375 (BrNiR), its genetically engineered 3- and 2-domain variants, and Br 2D NiR revealing up to ~ 500-fold difference in catalytic efficiency in comparison with classical 2-domain CuNiRs. Contrary to the expectation that tethering would enhance electron delivery by restricting the conformational search by having a self-contained donor-acceptor system, we demonstrate that 4-domain BrNiR utilizes N-terminal tethering for downregulating enzymatic activity instead. Both Br 2D NiR and an engineered 2-domain variant of BrNiR (Δ(Cytc-Cup) BrNiR) have 3 to 5% NiR activity compared to the well-characterized 2-domain CuNiRs from Alcaligenes xylosoxidans (AxNiR) and Achromobacter cycloclastes (AcNiR). Structural comparison of Δ(Cytc-Cup) BrNiR and Br 2D NiR with classical 2-domain AxNiR and AcNiR reveals structural differences of the proton transfer pathway that could be responsible for the lowering of activity. Our study provides insights into unique structural and functional characteristics of naturally occurring 4-domain CuNiR and its engineered 3- and 2-domain variants. The reverse protein engineering approach utilized here has shed light onto the broader question of the evolution of transient encounter complexes and tethered electron transfer complexes. ENZYME: Copper-containing nitrite reductase (CuNiR) (EC 1.7.2.1). DATABASE: The atomic coordinate and structure factor of Δ(Cytc-Cup) BrNiR and Br 2D NiR have been deposited in the Protein Data Bank (http://www.rcsb.org/) under the accession code 6THE and 6THF, respectively.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Copper-containing nitrite reductaseA347Bradyrhizobium sp. ORS 375Mutation(s): 0 
Gene Names: nirKBRAO375_4030011
EC: 1.7.2.1
Find proteins for H0SLX7 (Bradyrhizobium sp. (strain ORS 375))
Explore H0SLX7 
Go to UniProtKB:  H0SLX7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.929α = 90
b = 106.929β = 90
c = 106.929γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
MOLREPphasing
ARP/wARPmodel building
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N013972/1

Revision History 

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references, Derived calculations