PDBsum entry 1d7e

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Photosynthesis PDB id
Protein chain
120 a.a. *
Waters ×151
* Residue conservation analysis
PDB id:
Name: Photosynthesis
Title: Crystal structure of the p65 crystal form of photoactive yellow protein
Structure: Photoactive yellow protein. Chain: a. Synonym: pyp. Engineered: yes
Source: Halorhodospira halophila. Organism_taxid: 1053. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.39Å     R-factor:   0.139     R-free:   0.198
Authors: D.M.F.Van Aalten,W.Crielaard,K.J.Hellingwerf,L.Joshua-Tor
Key ref: D.M.van Aalten et al. (2000). Conformational substates in different crystal forms of the photoactive yellow protein--correlation with theoretical and experimental flexibility. Protein Sci, 9, 64-72. PubMed id: 10739248 DOI: 10.1110/ps.9.1.64
17-Oct-99     Release date:   31-Mar-00    
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Protein chain
Pfam   ArchSchema ?
P16113  (PYP_HALHA) -  Photoactive yellow protein
125 a.a.
120 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: 10.1110/ps.9.1.64 Protein Sci 9:64-72 (2000)
PubMed id: 10739248  
Conformational substates in different crystal forms of the photoactive yellow protein--correlation with theoretical and experimental flexibility.
D.M.van Aalten, W.Crielaard, K.J.Hellingwerf, L.Joshua-Tor.
The conformational changes during the photocycle of the photoactive yellow protein have been the subject of many recent studies. Spectroscopic measurements have shown that the photocycle also occurs in a crystalline environment, and this has been the basis for subsequent Laue diffraction and cryocrystallographic studies. These studies have shown that conformational changes during the photocycle are limited to the chromophore and its immediate environment. However, spectroscopic studies suggest the presence of large conformational changes in the protein. Here, we address this apparent discrepancy in two ways. First, we obtain a description of large concerted motions in the ground state of the yellow protein from NMR data and theoretical calculations. Second, we describe the high-resolution structure of the yellow protein crystallized in a different space group. The structure of the yellow protein differs significantly between the two crystal forms. We show that these differences can be used to obtain a description of the flexibility of the protein that is consistent with the motions observed in solution.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19472177 Q.Zhao (2009).
Protein thermodynamic structure.
  IUBMB Life, 61, 600-606.  
17680690 D.A.Kondrashov, W.Zhang, R.Aranda, B.Stec, and G.N.Phillips (2008).
Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments.
  Proteins, 70, 353-362.
PDB codes: 1jw8 1u7r 1u7s
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.  
15009198 M.H.Hefti, K.J.Françoijs, Vries, R.Dixon, and J.Vervoort (2004).
The PAS fold. A redefinition of the PAS domain based upon structural prediction.
  Eur J Biochem, 271, 1198-1208.  
15583378 M.Sugishima, N.Tanimoto, K.Soda, N.Hamada, F.Tokunaga, and K.Fukuyama (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.
PDB code: 1ugu
15159559 S.Anderson, S.Crosson, and K.Moffat (2004).
Short hydrogen bonds in photoactive yellow protein.
  Acta Crystallogr D Biol Crystallogr, 60, 1008-1016.
PDB codes: 1ot6 1ot9 1ota 1otb 1otd 1ote 1oti
14997553 Z.Kovári, and M.Vas (2004).
Protein conformer selection by sequence-dependent packing contacts in crystals of 3-phosphoglycerate kinase.
  Proteins, 55, 198-209.  
12945053 A.Merlino, L.Vitagliano, M.A.Ceruso, and L.Mazzarella (2003).
Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin.
  Proteins, 53, 101-110.  
12590594 E.Chen, T.Gensch, A.B.Gross, J.Hendriks, K.J.Hellingwerf, and D.S.Kliger (2003).
Dynamics of protein and chromophore structural changes in the photocycle of photoactive yellow protein monitored by time-resolved optical rotatory dispersion.
  Biochemistry, 42, 2062-2071.  
12718516 M.A.Cusanovich, and T.E.Meyer (2003).
Photoactive yellow protein: a prototypic PAS domain sensory protein and development of a common signaling mechanism.
  Biochemistry, 42, 4759-4770.  
12945580 R.Kort, R.B.Ravelli, F.Schotte, D.Bourgeois, W.Crielaard, K.J.Hellingwerf, and M.Wulff (2003).
Characterization of photocycle intermediates in crystalline photoactive yellow protein.
  Photochem Photobiol, 78, 131-137.  
12563032 S.Rajagopal, and K.Moffat (2003).
Crystal structure of a photoactive yellow protein from a sensor histidine kinase: conformational variability and signal transduction.
  Proc Natl Acad Sci U S A, 100, 1649-1654.
PDB code: 1mzu
11914481 D.M.van Aalten, W.Crielaard, K.J.Hellingwerf, and L.Joshua-Tor (2002).
Structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 A resolution.
  Acta Crystallogr D Biol Crystallogr, 58, 585-590.
PDB code: 1kou
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.