PDBsum entry 1ot9

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Luminescent protein PDB id
Protein chain
125 a.a. *
Waters ×193
* Residue conservation analysis
PDB id:
Name: Luminescent protein
Title: Cryotrapped state in wild type photoactive yellow protein, i with continuous illumination at 110k
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
1.00Å     R-factor:   0.134     R-free:   0.161
Ensemble: 2 models
Authors: S.Anderson,S.Crosson,K.Moffat
Key ref:
S.Anderson et al. (2004). Short hydrogen bonds in photoactive yellow protein. Acta Crystallogr D Biol Crystallogr, 60, 1008-1016. PubMed id: 15159559 DOI: 10.1107/S090744490400616X
21-Mar-03     Release date:   11-May-04    
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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/S090744490400616X Acta Crystallogr D Biol Crystallogr 60:1008-1016 (2004)
PubMed id: 15159559  
Short hydrogen bonds in photoactive yellow protein.
S.Anderson, S.Crosson, K.Moffat.
Eight high-resolution crystal structures of the ground state of photoactive yellow protein (PYP) solved under a variety of conditions reveal that its chromophore is stabilized by two unusually short hydrogen bonds. Both Tyr42 Oeta and Glu46 Oepsilon are separated from the chromophore phenolate oxygen by less than the sum of their atomic van der Waals radii, 2.6 angstroms. This is characteristic of strong hydrogen bonding, in which hydrogen bonds acquire significant covalent character. The hydrogen bond from the protonated Glu46 to the negatively charged phenolate oxygen is 2.58 +/- 0.01 angstroms in length, while that from Tyr42 is considerably shorter, 2.49 +/- 0.01 angstroms. The E46Q mutant was solved to 0.95 angstroms resolution; the isosteric mutation increased the length of the hydrogen bond from Glx46 to the chromophore by 0.29 +/- 0.01 angstroms to that of an average hydrogen bond, 2.88 +/- 0.01 angstroms. The very short hydrogen bond from Tyr42 explains why mutating this residue has such a severe effect on the ground-state structure and PYP photocycle. The effect of isosteric mutations on the photocycle can be largely explained by the alterations to the length and strength of these hydrogen bonds.
  Selected figure(s)  
Figure 1.
Figure 1 The ground-state coumaric acid chromophore (pCA) and its binding pocket in wild-type PYP. Hydrogen bonds are shown as dashed lines.
Figure 5.
Figure 5 Difference electron-density maps between wild type and E46Q mutant in space group P6[3] superimposed on the wild-type structure. Red contours denote negative difference electron density and blue denote positive. The entire molecule contoured at 5 is shown at (a) 110 K and (b) at 295 K. The chromophore-binding pocket contoured at 4 and 8 is shown at (c) 110 K and (d) at 295 K.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 1008-1016) copyright 2004.  
  Figures were 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.  
20192744 A.Möglich, X.Yang, R.A.Ayers, and K.Moffat (2010).
Structure and function of plant photoreceptors.
  Annu Rev Plant Biol, 61, 21-47.  
19244251 G.Minasov, S.Padavattan, L.Shuvalova, J.S.Brunzelle, D.J.Miller, A.Baslé, C.Massa, F.R.Collart, T.Schirmer, and W.F.Anderson (2009).
Crystal Structures of YkuI and Its Complex with Second Messenger Cyclic Di-GMP Suggest Catalytic Mechanism of Phosphodiester Bond Cleavage by EAL Domains.
  J Biol Chem, 284, 13174-13184.
PDB codes: 2bas 2w27
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.  
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
18338342 A.Jezierska, J.J.Panek, and A.Koll (2008).
Spectroscopic properties of a strongly anharmonic Mannich base N-oxide.
  Chemphyschem, 9, 839-846.  
18309395 K.Koike, K.Kawaguchi, and T.Yamato (2008).
Stress tensor analysis of the protein quake of photoactive yellow protein.
  Phys Chem Chem Phys, 10, 1400-1405.  
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.  
18808119 P.A.Sigala, D.A.Kraut, J.M.Caaveiro, B.Pybus, E.A.Ruben, D.Ringe, G.A.Petsko, and D.Herschlag (2008).
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.
  J Am Chem Soc, 130, 13696-13708.
PDB codes: 2inx 3cpo
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.  
16952373 R.Brudler, C.R.Gessner, S.Li, S.Tyndall, E.D.Getzoff, and V.L.Woods (2006).
PAS domain allostery and light-induced conformational changes in photoactive yellow protein upon I2 intermediate formation, probed with enhanced hydrogen/deuterium exchange mass spectrometry.
  J Mol Biol, 363, 148-160.  
16513787 S.Yeremenko, I.H.van Stokkum, K.Moffat, and K.J.Hellingwerf (2006).
Influence of the crystalline state on photoinduced dynamics of photoactive yellow protein studied by ultraviolet-visible transient absorption spectroscopy.
  Biophys J, 90, 4224-4235.  
15870207 H.Ihee, S.Rajagopal, V.Srajer, R.Pahl, S.Anderson, M.Schmidt, F.Schotte, P.A.Anfinrud, M.Wulff, and K.Moffat (2005).
Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds.
  Proc Natl Acad Sci U S A, 102, 7145-7150.
PDB codes: 1ts0 1ts6 1ts7 1ts8
15642261 S.Rajagopal, S.Anderson, V.Srajer, M.Schmidt, R.Pahl, and K.Moffat (2005).
A structural pathway for signaling in the E46Q mutant of photoactive yellow protein.
  Structure, 13, 55-63.
PDB codes: 1t18 1t19 1t1a 1t1b 1t1c
15819878 S.Rajagopal, and S.Vishveshwara (2005).
Short hydrogen bonds in proteins.
  FEBS J, 272, 1819-1832.  
15274923 S.Anderson, V.Srajer, R.Pahl, S.Rajagopal, F.Schotte, P.Anfinrud, M.Wulff, and K.Moffat (2004).
Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein.
  Structure, 12, 1039-1045.
PDB codes: 1s1y 1s1z
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.