6ZUI | pdb_00006zui

Crystal structure of the Cys-Ser mutant of the cpYFP-based biosensor for hypochlorous acid

• PDB DOI: https://doi.org/10.2210/pdb6ZUI/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Escherichia coli K-12, Aequorea victoria
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-07-23 Released: 2021-06-30 
• Deposition Author(s): Tossounian, M.A., Van Molle, I., Messens, J.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Models: experimental

Literature

Hypocrates is a genetically encoded fluorescent biosensor for (pseudo)hypohalous acids and their derivatives.

Kostyuk, A.I., Tossounian, M.A., Panova, A.S., Thauvin, M., Raevskii, R.I., Ezerina, D., Wahni, K., Van Molle, I., Sergeeva, A.D., Vertommen, D., Gorokhovatsky, A.Y., Baranov, M.S., Vriz, S., Messens, J., Bilan, D.S., Belousov, V.V.

(2022) Nat Commun 13: 171-171

• PubMed: 35013284 
• DOI: https://doi.org/10.1038/s41467-021-27796-2
• Primary Citation of Related Structures:  
  6ZUI


• PubMed Abstract: 
  

  The lack of tools to monitor the dynamics of (pseudo)hypohalous acids in live cells and tissues hinders a better understanding of inflammatory processes. Here we present a fluorescent genetically encoded biosensor, Hypocrates, for the visualization of (pseudo)hypohalous acids and their derivatives. Hypocrates consists of a circularly permuted yellow fluorescent protein integrated into the structure of the transcription repressor NemR from Escherichia coli. We show that Hypocrates is ratiometric, reversible, and responds to its analytes in the 10 ⁶  M ^-1 s ^-1 range. Solving the Hypocrates X-ray structure provided insights into its sensing mechanism, allowing determination of the spatial organization in this circularly permuted fluorescent protein-based redox probe. We exemplify its applicability by imaging hypohalous stress in bacteria phagocytosed by primary neutrophils. Finally, we demonstrate that Hypocrates can be utilized in combination with HyPerRed for the simultaneous visualization of (pseudo)hypohalous acids and hydrogen peroxide dynamics in a zebrafish tail fin injury model.

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Organizational Affiliation: 
• Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia.
Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997, Moscow, Russia.
Laboratory of Experimental Oncology, Pirogov Russian National Research Medical University, 117997, Moscow, Russia.
VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium.
Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium.
Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium.
Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom.
Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, 75231, France.
Sorbonne Université, Collège Doctoral, Paris, 75005, France.
Biological Department, Lomonosov Moscow State University, 119992, Moscow, Russia.
de Duve Institute, MASSPROT platform, UCLouvain, 1200, Brussels, Belgium.
Laboratory of Medicinal Substances Chemistry, Pirogov Russian National Research Medical University, 117997, Moscow, Russia.
Université de Paris, Paris, 75006, France.
Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium. [e-mail].
Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium. [e-mail].
Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium. [e-mail].
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia. [e-mail].
Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997, Moscow, Russia. [e-mail].
Laboratory of Experimental Oncology, Pirogov Russian National Research Medical University, 117997, Moscow, Russia. [e-mail].
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia. [e-mail].
Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997, Moscow, Russia. [e-mail].
Laboratory of Experimental Oncology, Pirogov Russian National Research Medical University, 117997, Moscow, Russia. [e-mail].
Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, 117997, Moscow, Russia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 49.63 kDa 
• Atom Count: 3,503 
• Modeled Residue Count: 421 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional repressor NemR,Green fluorescent protein,Green fluorescent protein,HTH-type transcriptional repressor NemR	A	446	Escherichia coli K-12, Aequorea victoria	Mutation(s): 19  Gene Names: nemR, ydhM, b1649, JW5874, GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212
Find proteins for P67430 (Escherichia coli (strain K12)) Explore P67430  Go to UniProtKB:  P67430
UniProt Groups	P42212P67430

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2	A	L-PEPTIDE LINKING	C13 H13 N3 O4		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.232	α = 90
b = 95.437	β = 90
c = 106.246	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Tossounian, M.A., Van Molle, I., Messens, J.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	--

Revision History  

• Version 1.0: 2021-06-30
  Type: Initial release
  
• Version 1.1: 2022-01-19
  Changes: Advisory, Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary