PDBsum entry 1ugu

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protein ligands links
Photosynthesis PDB id
Jmol PyMol
Protein chain
122 a.a. *
Waters ×180
* Residue conservation analysis
PDB id:
Name: Photosynthesis
Title: Crystal structure of pyp e46q mutant
Structure: Photoactive yellow protein. Chain: a. Synonym: pyp. Engineered: yes. Mutation: yes
Source: Halorhodospira halophila. Organism_taxid: 1053. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.20Å     R-factor:   0.167     R-free:   0.191
Authors: M.Sugishima,Y.Tanimoto,N.Hamada,F.Tokunaga,K.Fukuyama
Key ref:
M.Sugishima et al. (2004). Structure of photoactive yellow protein (PYP) E46Q mutant at 1.2 A resolution suggests how Glu46 controls the spectroscopic and kinetic characteristics of PYP. Acta Crystallogr D Biol Crystallogr, 60, 2305-2309. PubMed id: 15583378 DOI: 10.1107/S0907444904024084
19-Jun-03     Release date:   10-Aug-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P16113  (PYP_HALHA) -  Photoactive yellow protein
125 a.a.
122 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to stimulus   4 terms 
  Biochemical function     photoreceptor activity     1 term  


DOI no: 10.1107/S0907444904024084 Acta Crystallogr D Biol Crystallogr 60:2305-2309 (2004)
PubMed id: 15583378  
Structure of photoactive yellow protein (PYP) E46Q mutant at 1.2 A resolution suggests how Glu46 controls the spectroscopic and kinetic characteristics of PYP.
M.Sugishima, N.Tanimoto, K.Soda, N.Hamada, F.Tokunaga, K.Fukuyama.
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.
  Selected figure(s)  
Figure 3.
Figure 3 Schematic diagram of p-coumaric acid and residues around the chromophore in (a) WT and (b) the E46Q mutant. Open arrows represent the localization of electrons of p-coumaric acid.
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 2305-2309) copyright 2004.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20220103 A.F.Philip, R.A.Nome, G.A.Papadantonakis, N.F.Scherer, and W.D.Hoff (2010).
Spectral tuning in photoactive yellow protein by modulation of the shape of the excited state energy surface.
  Proc Natl Acad Sci U S A, 107, 5821-5826.  
18399917 M.Kumauchi, M.T.Hara, P.Stalcup, A.Xie, and W.D.Hoff (2008).
Identification of six new photoactive yellow proteins--diversity and structure-function relationships in a bacterial blue light photoreceptor.
  Photochem Photobiol, 84, 956-969.  
17487311 M.A.van der Horst, J.C.Arents, R.Kort, and K.J.Hellingwerf (2007).
Binding, tuning and mechanical function of the 4-hydroxy-cinnamic acid chromophore in photoactive yellow protein.
  Photochem Photobiol Sci, 6, 571-579.  
17015839 L.J.van Wilderen, M.A.van der Horst, I.H.van Stokkum, K.J.Hellingwerf, R.van Grondelle, and M.L.Groot (2006).
Ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein.
  Proc Natl Acad Sci U S A, 103, 15050-15055.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.