PDBsum entry 2qws

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Signaling protein PDB id
Protein chain
125 a.a. *
DOD ×68
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Neutron and x-ray structural studies of short hydrogen bonds photoactive yellow protein (pyp)
Structure: Photoactive yellow protein. Chain: a. Synonym: pyp. Engineered: yes
Source: Halorhodospira halophila. Organism_taxid: 1053. Strain: bn9626. Gene: pyp
2.50Å     R-factor:   0.262     R-free:   0.273
Authors: S.Z.Fisher,P.Langan
Key ref:
S.Z.Fisher et al. (2007). Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP). Acta Crystallogr D Biol Crystallogr, 63, 1178-1184. PubMed id: 18007033 DOI: 10.1107/S0907444907047646
10-Aug-07     Release date:   18-Mar-08    
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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: 10.1107/S0907444907047646 Acta Crystallogr D Biol Crystallogr 63:1178-1184 (2007)
PubMed id: 18007033  
Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP).
S.Z.Fisher, S.Anderson, R.Henning, K.Moffat, P.Langan, P.Thiyagarajan, A.J.Schultz.
Photoactive yellow protein (PYP) from Halorhodospira halophila is a soluble 14 kDa blue-light photoreceptor. It absorbs light via its para-coumaric acid chromophore (pCA), which is covalently attached to Cys69 and is believed to be involved in the negative phototactic response of the organism to blue light. The complete structure (including H atoms) of PYP has been determined in D(2)O-soaked crystals through the application of joint X-ray (1.1 A) and neutron (2.5 A) structure refinement in combination with cross-validated maximum-likelihood simulated annealing. The resulting XN structure reveals that the phenolate O atom of pCA accepts deuterons from Glu46 O(epsilon2) and Tyr42 O(eta) in two unusually short hydrogen bonds. This arrangement is stabilized by the donation of a deuteron from Thr50 O(gamma1) to Tyr42 O(eta). However, the deuteron position between pCA and Tyr42 is only partially occupied. Thus, this atom may also interact with Thr50, possibly being disordered or fluctuating between the two bonds.
  Selected figure(s)  
Figure 1.
Figure 1 Cross-eye stereoview of the chromophore-binding pocket and active-site architecture. (a) Hydrogen bond between Glu46 and pCA; (b) hydrogen bond between Glu46 and pCA; (c) hydrogen bond between pCA, Thr50 and Tyr42. Binding-pocket residues and pCA are shown in yellow ball-and-stick representation. The 2F[o] - F[c] nuclear map is shown in green mesh (contoured at 1.2 ), the F[o] - F[c] nuclear map in orange and the 2F[o] - F[c] electron-density map in red mesh (contoured at 1.2 ). Blue arrows indicate hydrogen bonds.
Figure 2.
Figure 2 Cross-eye stereoview of solvent and protonated-residue interactions. (a) Interaction between His3, Asp36 and Tyr76; (b) interaction of protonated His108 and Asp89 with W1; (c) interaction of protonated Trp119 with W4. The 2F[o] - F[c] electron-density maps are shown in red mesh (contoured at 1.5 ) and the 2F[o] - F[c] nuclear density in green mesh (contoured at 1.5 ).
  The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 1178-1184) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19551213 D.Hoersch, H.Otto, M.A.Cusanovich, and M.P.Heyn (2009).
Time-resolved spectroscopy of dye-labeled photoactive yellow protein suggests a pathway of light-induced structural changes in the N-terminal cap.
  Phys Chem Chem Phys, 11, 5437-5444.  
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.  
19465771 P.D.Adams, M.Mustyakimov, P.V.Afonine, and P.Langan (2009).
Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.
  Acta Crystallogr D Biol Crystallogr, 65, 567-573.  
19122140 S.Yamaguchi, H.Kamikubo, K.Kurihara, R.Kuroki, N.Niimura, N.Shimizu, Y.Yamazaki, and M.Kataoka (2009).
Low-barrier hydrogen bond in photoactive yellow protein.
  Proc Natl Acad Sci U S A, 106, 440-444.
PDB codes: 2zoh 2zoi
  19407386 S.Z.Fisher, A.Y.Kovalevsky, J.F.Domsic, M.Mustyakimov, D.N.Silverman, R.McKenna, and P.Langan (2009).
Preliminary joint neutron and X-ray crystallographic study of human carbonic anhydrase II.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 495-498.  
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