Biological Assembly 1  

 3D View: Structure | Electron Density | 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)

Macromolecule Content

• Total Structure Weight: 111.44 kDa 
• Atom Count: 8248 
• Residue Count: 1009 
• Unique protein chains: 1

5F7B

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

• DOI: 10.2210/pdb5F7B/pdb

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


• Deposited: 2015-12-07 Released: 2016-03-16 
• Deposition Author(s): 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.

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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 

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

• PubMed: 26929369 
• 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 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.

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Organizational Affiliation: 

Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A, B, C	342	Alcaligenes faecalis	Mutation(s): 0  Gene Names: nirK, nir EC: 1.7.2.1
Find proteins for P38501 (Alcaligenes faecalis) Explore P38501  Go to UniProtKB:  P38501

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	A, B, C	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

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 = 62.836	α = 90
b = 103.511	β = 90
c = 147.246	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-12-07 
• Released Date: 2016-03-16 
Deposition Author(s): 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.

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