Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 14.05 kDa 
• Atom Count: 1129 
• Modelled Residue Count: 125 
• Deposited Residue Count: 125 
• Unique protein chains: 1

5GX9

PYP mutant - E46Q

• PDB DOI: 10.2210/pdb5GX9/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Halorhodospira halophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-09-16 Released: 2017-08-30 
• Deposition Author(s): Yonezawa, K.
• Funding Organization(s): Japanese Ministry of Education, Culture, Sports, Science and Technology

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.200 
• R-Value Work: 0.158 
• R-Value Observed: 0.162 

Literature

Neutron crystallography of photoactive yellow protein reveals unusual protonation state of Arg52 in the crystal

Yonezawa, K., Shimizu, N., Kurihara, K., Yamazaki, Y., Kamikubo, H., Kataoka, M.

(2017) Sci Rep 7: 9361-9361

• PubMed: 28839266 
• DOI: 10.1038/s41598-017-09718-9
• Primary Citation of Related Structures:  
  5GX9


• PubMed Abstract: 
  

Because of its high pK _a , arginine (Arg) is believed to be protonated even in the hydrophobic environment of the protein interior. However, our neutron crystallographic structure of photoactive yellow protein, a light sensor, demonstrated that Arg52 adopts an electrically neutral form. We also showed that the hydrogen bond between the chromophore and Glu46 is a so-called low barrier hydrogen bond (LBHB). Because both the neutral Arg and LBHB are unusual in proteins, these observations remain controversial. To validate our findings, we carried out neutron crystallographic analysis of the E46Q mutant of PYP. The resultant structure revealed that the proportion of the cationic form is higher in E46Q than in WT, although the cationic and neutral forms of Arg52 coexist in E46Q. These observations were confirmed by the occupancy of the deuterium atom bound to the N _η1 atom combined with an alternative conformation of the N _(η2) D ₂ group comprising sp ² hybridisation. Based on these results, we propose that the formation of the LBHB decreases the proton affinity of Arg52, stabilizing the neutral form in the crystal.

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Organizational Affiliation: 

Comprehensive Research Organization for Science and Society, Research Center for Neutron Science and Technology, 162-1 Shirakata, Tokai, Ibaraki, 319-1106, Japan. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photoactive yellow protein	A	125	Halorhodospira halophila	Mutation(s): 1  Gene Names: pyp
UniProt
Find proteins for P16113 (Halorhodospira halophila) Explore P16113  Go to UniProtKB:  P16113

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HC4	B [auth A]	4'-HYDROXYCINNAMIC ACID C9 H8 O3 NGSWKAQJJWESNS-ZZXKWVIFSA-N

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.200 
• R-Value Work: 0.158 
• R-Value Observed: 0.162 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.823	α = 90
b = 66.823	β = 90
c = 40.982	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
AMoRE	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-09-16 
• Released Date: 2017-08-30 
Deposition Author(s): Yonezawa, K.

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Funding Organization	Location	Grant Number
Japanese Ministry of Education, Culture, Sports, Science and Technology	Japan	25102003

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Database references
• Version 1.2: 2018-11-28
  Changes: Data collection