Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 35.95 kDa 
• Atom Count: 2986 
• Modelled Residue Count: 298 
• Deposited Residue Count: 323 
• Unique protein chains: 1

6L46

High-resolution neutron and X-ray joint refined structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans

• PDB DOI: 10.2210/pdb6L46/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Geobacillus thermodenitrificans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-16 Released: 2020-02-12 
• Deposition Author(s): Fukuda, Y., Hirano, Y., Kusaka, K., Inoue, T., Tamada, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.112 
• R-Value Work: 0.097 
• R-Value Observed: 0.098 

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• Method: NEUTRON DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.159 
• R-Value Work: 0.142 
• R-Value Observed: 0.142 

Literature

High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase.

Fukuda, Y., Hirano, Y., Kusaka, K., Inoue, T., Tamada, T.

(2020) Proc Natl Acad Sci U S A 117: 4071-4077

• PubMed: 32041886 
• DOI: 10.1073/pnas.1918125117
• Primary Citation of Related Structures:  
  6L46


• PubMed Abstract: 
  

Copper-containing nitrite reductases (CuNIRs) transform nitrite to gaseous nitric oxide, which is a key process in the global nitrogen cycle. The catalytic mechanism has been extensively studied to ultimately achieve rational control of this important geobiochemical reaction. However, accumulated structural biology data show discrepancies with spectroscopic and computational studies; hence, the reaction mechanism is still controversial. In particular, the details of the proton transfer involved in it are largely unknown. This situation arises from the failure of determining positions of hydrogen atoms and protons, which play essential roles at the catalytic site of CuNIRs, even with atomic resolution X-ray crystallography. Here, we determined the 1.50 Å resolution neutron structure of a CuNIR from Geobacillus thermodenitrificans (trimer molecular mass of ∼106 kDa) in its resting state at low pH. Our neutron structure reveals the protonation states of catalytic residues (deprotonated aspartate and protonated histidine), thus providing insights into the catalytic mechanism. We found that a hydroxide ion can exist as a ligand to the catalytic Cu atom in the resting state even at a low pH. This OH-bound Cu site is unexpected from previously given X-ray structures but consistent with a reaction intermediate suggested by computational chemistry. Furthermore, the hydrogen-deuterium exchange ratio in our neutron structure suggests that the intramolecular electron transfer pathway has a hydrogen-bond jump, which is proposed by quantum chemistry. Our study can seamlessly link the structural biology to the computational chemistry of CuNIRs, boosting our understanding of the enzymes at the atomic and electronic levels.

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Organizational Affiliation: 

Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 319-1106 Tokai, Ibaraki, Japan; [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A	323	Geobacillus thermodenitrificans	Mutation(s): 0  Gene Names: nirK, GTHT12_00198 EC: 1.7.2.1
UniProt
Find proteins for A0A1W6VP04 (Geobacillus thermodenitrificans) Explore A0A1W6VP04  Go to UniProtKB:  A0A1W6VP04

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	H [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CU (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.112 
• R-Value Work: 0.097 
• R-Value Observed: 0.098 
• Space Group: H 3
• Diffraction Data DOI: 10.18430/m36l46 Protein Diffraction

• Method: NEUTRON DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.159 
• R-Value Work: 0.142 
• R-Value Observed: 0.142 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.212	α = 90
b = 114.212	β = 90
c = 83.688	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
STARGazer	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-10-16 
• Released Date: 2020-02-12 
Deposition Author(s): Fukuda, Y., Hirano, Y., Kusaka, K., Inoue, T., Tamada, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	--

Revision History  

• Version 1.0: 2020-02-12
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Database references
• Version 1.2: 2020-03-11
  Changes: Database references