5F7B

Resting state structure of CuNiR form Alcaligenes faecalis determined at 293 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.P.Inoue, T.Iwata, S.Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

  • DOI: 10.1073/pnas.1517770113
  • Primary Citation of Related Structures:  
    5F7B, 5D4H, 5D4J, 5D4I, 4YSC, 4YSE, 5F7A

  • 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; inouet@chem.eng.osaka-u.ac.jp mizohata@chem.eng.osaka-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Copper-containing nitrite reductaseA, B, C342Alcaligenes faecalisMutation(s): 0 
Gene Names: nirKnir
EC: 1.7.2.1
Find proteins for P38501 (Alcaligenes faecalis)
Explore P38501 
Go to UniProtKB:  P38501
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download CCD File 
A, B, C
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.836α = 90
b = 103.511β = 90
c = 147.246γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Database references, Derived calculations