6THF

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

DOI: 10.2210/pdb6THF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bradyrhizobium sp. ORS 375
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-11-20 Released: 2020-04-22
Deposition Author(s): Sasaki, D., Watanabe, T.F., Eady, R.R., Garratt, R.C., Antonyuk, S.V., Hasnain, S.S.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

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

PubMed: 32255260 Search on PubMed
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 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
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A	347	Bradyrhizobium sp. ORS 375	Mutation(s): 0 Gene Names: nirK, BRAO375_4030011 EC: 1.7.2.1
Find proteins for H0SLX7 (Bradyrhizobium sp. (strain ORS 375)) Explore H0SLX7 Go to UniProtKB: H0SLX7
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain B [A] SDF format, chain C [A] MOL2 format, chain B [A] MOL2 format, chain C [A]	A	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain E [A] SDF format, chain F [A] SDF format, chain G [A] SDF format, chain H [A] SDF format, chain I [A] SDF format, chain J [A] SDF format, chain K [A] MOL2 format, chain D [A] MOL2 format, chain E [A] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain H [A] MOL2 format, chain I [A] MOL2 format, chain J [A] MOL2 format, chain K [A]	A	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain L [A] SDF format, chain M [A] MOL2 format, chain L [A] MOL2 format, chain M [A]	A	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Ligand Interaction