PDBsum entry 2d01

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protein ligands links
Signaling protein PDB id
Protein chain
124 a.a. *
Waters ×210
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Wild type photoactive yellow protein, p65 form
Structure: Photoactive yellow protein. Chain: a. Synonym: photoreceptor, pyp. Engineered: yes
Source: Halorhodospira halophila. Organism_taxid: 1053. Gene: pyp. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.34Å     R-factor:   0.154     R-free:   0.189
Authors: N.Shimizu,H.Kamikubo,Y.Yamazaki,Y.Imamoto,M.Kataoka
Key ref:
N.Shimizu et al. (2006). The crystal structure of the R52Q mutant demonstrates a role for R52 in chromophore pKa regulation in photoactive yellow protein. Biochemistry, 45, 3542-3547. PubMed id: 16533035 DOI: 10.1021/bi051430a
21-Jul-05     Release date:   04-Apr-06    
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Protein chain
Pfam   ArchSchema ?
P16113  (PYP_HALHA) -  Photoactive yellow protein
125 a.a.
124 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to stimulus   5 terms 
  Biochemical function     signal transducer activity     2 terms  


DOI no: 10.1021/bi051430a Biochemistry 45:3542-3547 (2006)
PubMed id: 16533035  
The crystal structure of the R52Q mutant demonstrates a role for R52 in chromophore pKa regulation in photoactive yellow protein.
N.Shimizu, H.Kamikubo, Y.Yamazaki, Y.Imamoto, M.Kataoka.
Mutating arginine 52 to glutamine (R52Q) in photoactive yellow protein (PYP) increases the pK(a) of the chromophore by 1 pH unit. The structure of the R52Q PYP mutant was determined by X-ray crystallography and was compared to the structure of wild-type PYP to assess the role of R52 in pK(a) regulation. The essential differences between R52Q and the wild type were confined to the loop region containing the 52nd residue. While the hydrogen bonds involving the chromophore were unchanged by the mutation, removing the guanidino group generated a cavity near the chromophore; this cavity is occupied by two water molecules. In the wild type, R52 forms hydrogen bonds with T50 and Y98; these hydrogen bonds are lost in R52Q. Q52 is linked to Y98 by hydrogen bonding through the two water molecules. R52 acts as a lid on the chromophore binding pocket and controls the accessibility of the exterior solvent and the pK(a) of the chromophore. R52 is found to flip out during the formation of PYP(M). The result of this movement is quite similar to the altered structure of R52Q. Thus, we propose that conformational changes at R52 are partly responsible for pK(a) regulation during the photocycle.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19091750 J.Hendriks, and K.J.Hellingwerf (2009).
pH Dependence of the Photoactive Yellow Protein Photocycle Recovery Reaction Reveals a New Late Photocycle Intermediate with a Deprotonated Chromophore.
  J Biol Chem, 284, 5277-5288.  
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.  
18399916 Y.Imamoto, M.Harigai, T.Morimoto, and M.Kataoka (2008).
Low-temperature spectroscopy of Met100Ala mutant of photoactive yellow protein.
  Photochem Photobiol, 84, 970-976.  
18227128 Y.Imamoto, S.Tatsumi, M.Harigai, Y.Yamazaki, H.Kamikubo, and M.Kataoka (2008).
Diverse roles of glycine residues conserved in photoactive yellow proteins.
  Biophys J, 94, 3620-3628.  
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.