PDBsum entry 2zoi

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Signaling protein PDB id
Protein chain
125 a.a. *
DOD ×73
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Neutron crystal structure of photoactive yellow protein, wil 295k
Structure: Photoactive yellow protein. Chain: a. Synonym: pyp. Engineered: yes
Source: Halorhodospira halophila. Organism_taxid: 1053. Gene: pyp. Expressed in: escherichia coli. Expression_system_taxid: 562.
Authors: S.Yamaguchi
Key ref:
S.Yamaguchi et al. (2009). Low-barrier hydrogen bond in photoactive yellow protein. Proc Natl Acad Sci U S A, 106, 440-444. PubMed id: 19122140 DOI: 10.1073/pnas.0811882106
21-May-08     Release date:   24-Mar-09    
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Protein chain
Pfam   ArchSchema ?
P16113  (PYP_HALHA) -  Photoactive yellow protein
125 a.a.
125 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: 10.1073/pnas.0811882106 Proc Natl Acad Sci U S A 106:440-444 (2009)
PubMed id: 19122140  
Low-barrier hydrogen bond in photoactive yellow protein.
S.Yamaguchi, H.Kamikubo, K.Kurihara, R.Kuroki, N.Niimura, N.Shimizu, Y.Yamazaki, M.Kataoka.
Low-barrier hydrogen bonds (LBHBs) have been proposed to play roles in protein functions, including enzymatic catalysis and proton transfer. Transient formation of LBHBs is expected to stabilize specific reaction intermediates. However, based on experimental results and theoretical considerations, arguments against the importance of LBHB in proteins have been raised. The discrepancy is caused by the absence of direct identification of the hydrogen atom position. Here, we show by high-resolution neutron crystallography of photoactive yellow protein (PYP) that a LBHB exists in a protein, even in the ground state. We identified approximately 87% (819/942) of the hydrogen positions in PYP and demonstrated that the hydrogen bond between the chromophore and E46 is a LBHB. This LBHB stabilizes an isolated electric charge buried in the hydrophobic environment of the protein interior. We propose that in the excited state the fast relaxation of the LBHB into a normal hydrogen bond is the trigger for photo-signal propagation to the protein moiety. These results give insights into the novel roles of LBHBs and the mechanism of the formation of LBHBs.
  Selected figure(s)  
Figure 2.
Hydrogen bonds in PYP. (A) Correlation of donor-H(D) and H(D)-acceptor bond lengths with the donor–acceptor distances and a histogram of hydrogen bond lengths. The open and closed triangles show the donor-H(D) and the H(D)-acceptor distances, respectively. The SHBs are shown as a red circle (pCA-E46) and a blue circle (pCA-Y42). The solid lines represent the calculated donor-H(D) distances, assuming bent angles of 120° and 180°, respectively. (B and C) The nuclear and electron density maps with the structure models of the two SHBs, pCA-E46 (B) and pCA-Y42 (C). The blue mesh represents the positive nuclear density of the deuterium atoms, contoured at 80% of the maximum peak height of the F[O] − F[C] difference maps omitting each deuterium atom involved in the hydrogen bond; contour levels of 80% of the maximum peak height correspond to 8.26 σ for pCA-E46 and 6.86 σ or pCA-Y42. The yellow mesh (contoured at 4.1 σ) and the red mesh (contoured at −5.3 σ) show the 2F[O] − F[C] electron density maps of the heavy atoms and the F[O] − F[C] difference nuclear density map omitting the hydrogen atoms, respectively.
Figure 3.
The mechanism of the stabilization of the isolated negative charge in the vicinity of the chromophore in a hydrophobic environment of PYP. (A) The neutralization by a counter ion, which is believed so far. We ruled out this mechanism by the finding that R52 is not protonated (Fig. 1E). (B) Strong bond strength of LBHB and charge delocalization caused by the quasi-covalent bond of LBHB stabilizes the energetic disadvantage of the isolated negative charge buried in the protein interior.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21308813 R.Chaudret, G.A.Cisneros, O.Parisel, and J.P.Piquemal (2011).
Unraveling low-barrier hydrogen bonds in complex systems with a simple quantum topological criterion.
  Chemistry, 17, 2833-2837.  
20652880 S.Re, T.Imai, J.Jung, S.Ten-No, and Y.Sugita (2011).
Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation.
  J Comput Chem, 32, 260-270.  
20143849 W.Childs, and S.G.Boxer (2010).
Proton affinity of the oxyanion hole in the active site of ketosteroid isomerase.
  Biochemistry, 49, 2725-2731.  
19656821 J.H.Lakey (2009).
Neutrons for biologists: a beginner's guide, or why you should consider using neutrons.
  J R Soc Interface, 6, S567-S573.  
19470452 P.A.Sigala, M.A.Tsuchida, and D.Herschlag (2009).
Hydrogen bond dynamics in the active site of photoactive yellow protein.
  Proc Natl Acad Sci U S A, 106, 9232-9237.  
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.