5D4H

High-resolution nitrite complex of a copper nitrite reductase determined by synchrotron radiation crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.123 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography

Fukuda, Y.Tse, K.M.Nakane, T.Nakatsu, T.Suzuki, M.Sugahara, M.Inoue, S.Masuda, T.Yumoto, F.Matsugaki, N.Nango, E.Tono, K.Joti, Y.Kameshima, T.Song, C.Hatsui, T.Yabashi, M.Nureki, O.Murphy, M.E.Inoue, T.Iwata, S.Mizohata, E.

(2016) Proc.Natl.Acad.Sci.USA 113: 2928-2933

  • DOI: 10.1073/pnas.1517770113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proton-coupled electron transfer (PCET), a ubiquitous phenomenon in biological systems, plays an essential role in copper nitrite reductase (CuNiR), the key metalloenzyme in microbial denitrification of the global nitrogen cycle. Analyses of the nitr ...

    Proton-coupled electron transfer (PCET), a ubiquitous phenomenon in biological systems, plays an essential role in copper nitrite reductase (CuNiR), the key metalloenzyme in microbial denitrification of the global nitrogen cycle. Analyses of the nitrite reduction mechanism in CuNiR with conventional synchrotron radiation crystallography (SRX) have been faced with difficulties, because X-ray photoreduction changes the native structures of metal centers and the enzyme-substrate complex. Using serial femtosecond crystallography (SFX), we determined the intact structures of CuNiR in the resting state and the nitrite complex (NC) state at 2.03- and 1.60-Å resolution, respectively. Furthermore, the SRX NC structure representing a transient state in the catalytic cycle was determined at 1.30-Å resolution. Comparison between SRX and SFX structures revealed that photoreduction changes the coordination manner of the substrate and that catalytically important His255 can switch hydrogen bond partners between the backbone carbonyl oxygen of nearby Glu279 and the side-chain hydroxyl group of Thr280. These findings, which SRX has failed to uncover, propose a redox-coupled proton switch for PCET. This concept can explain how proton transfer to the substrate is involved in intramolecular electron transfer and why substrate binding accelerates PCET. Our study demonstrates the potential of SFX as a powerful tool to study redox processes in metalloenzymes.


    Organizational Affiliation

    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Copper-containing nitrite reductase
A, B, C
342Alcaligenes faecalisMutation(s): 0 
Gene Names: nirK (nir)
EC: 1.7.2.1
Find proteins for P38501 (Alcaligenes faecalis)
Go to UniProtKB:  P38501
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NO2
Query on NO2

Download SDF File 
Download CCD File 
A, B
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A, B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.123 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.419α = 90.00
b = 102.174β = 90.00
c = 145.791γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan--
X-ray Free-Electron Laser Priority Strategy ProgramJapan--

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references