Crystal structure of PYP E46Q mutant

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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This is version 1.4 of the entry. See complete history


Structure of photoactive yellow protein (PYP) E46Q mutant at 1.2 A resolution suggests how Glu46 controls the spectroscopic and kinetic characteristics of PYP.

Sugishima, M.Tanimoto, N.Soda, K.Hamada, N.Tokunaga, F.Fukuyama, K.

(2004) Acta Crystallogr D Biol Crystallogr 60: 2305-2309

  • DOI: https://doi.org/10.1107/S0907444904024084
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Photoactive yellow protein from Ectothiorhodospira halophila is a photoreceptor protein involved in the negative phototaxis of this bacterium. Its chromophore (p-coumaric acid) is deprotonated in the ground state, which is stabilized by a hydrogen-bond network between Tyr42, Glu46 and Thr50. Glu46 is a key residue as it has been suggested that the proton at Glu46 is transferred to the chromophore during its photoconversion from the dark state to the signalling state. The structure of E46Q mutant protein was determined at 1.2 A resolution, revealing that the phenolic O atom of p-coumaric acid is hydrogen bonded to NH(2) of Gln46 in E46Q with a longer distance (2.86 +/- 0.02 A) than its distance (2.51 A) to Glu46 OH in the wild type. This and the decreased thermal stability of E46Q relative to the wild type show that this hydrogen bond is weakened in the E46Q mutant compared with the corresponding bond in the wild type. Several characteristic features of E46Q such as an alkali shift in the pK(a) and the rapid photocycle can be explained by this weakened hydrogen bond. Furthermore, the red shift in the absorption maximum in E46Q can be explained by the delocalization of the electron on the phenolic oxygen of p-coumaric acid owing to the weakening of this hydrogen bond.

  • Organizational Affiliation

    Department of Biology, Graduate School of Science, Osaka University, Machikaneyama-cho 1-1, Toyonaka, Osaka 560-0043, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOACTIVE YELLOW PROTEIN125Halorhodospira halophilaMutation(s): 1 
Find proteins for P16113 (Halorhodospira halophila)
Explore P16113 
Go to UniProtKB:  P16113
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16113
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HC4

Download Ideal Coordinates CCD File 
C9 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.352α = 90
b = 40.352β = 90
c = 118.001γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description