6L46

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


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 

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

    Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 319-1106 Tokai, Ibaraki, Japan; t_inoue@phs.osaka-u.ac.jp tamada.taro@qst.go.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Copper-containing nitrite reductaseA323Geobacillus thermodenitrificansMutation(s): 0 
Gene Names: nirKGTHT12_00198
EC: 1.7.2.1
UniProt
Find proteins for A0A1W6VP04 (Geobacillus thermodenitrificans)
Explore A0A1W6VP04 
Go to UniProtKB:  A0A1W6VP04
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1W6VP04
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
H [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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 = 114.212α = 90
b = 114.212β = 90
c = 83.688γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
STARGazerdata reduction

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan--

Revision History  (Full details and data files)

  • 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