3PHY

PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED), SOLUTION STRUCTURE, NMR, 26 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 26 
  • Selection Criteria: LOW ENERGY 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure and backbone dynamics of the photoactive yellow protein.

Dux, P.Rubinstenn, G.Vuister, G.W.Boelens, R.Mulder, F.A.Hard, K.Hoff, W.D.Kroon, A.R.Crielaard, W.Hellingwerf, K.J.Kaptein, R.

(1998) Biochemistry 37: 12689-12699

  • DOI: 10.1021/bi9806652

  • PubMed Abstract: 
  • The solution structure of photoactive yellow protein (PYP), a photosensory protein from Ectothiorhodospira halophila, has been determined by multidimensional NMR spectroscopy. The structure consists of an open, twisted, 6-stranded, antiparallel beta- ...

    The solution structure of photoactive yellow protein (PYP), a photosensory protein from Ectothiorhodospira halophila, has been determined by multidimensional NMR spectroscopy. The structure consists of an open, twisted, 6-stranded, antiparallel beta-sheet, which is flanked by four alpha-helices on both sides. The final set of 26 selected structures is well-defined for the regions spanning residues Phe6-Ala16, Asp24-Ala112, and Tyr118-Val125 and displays a root-mean-square deviation, versus the average, of 0.45 A for the backbone and 0.88 A for all heavy atoms. Comparison of the solution structure with an earlier published 1.4 A crystal structure (Borgstahl, G. E. O., Williams, D. R., and Getzoff, E. D. (1995) Biochemistry 34, 6278-6287) reveals a similarity with a root-mean-square deviation of 1.77 A for the backbone for the well-defined regions. The most distinct difference in the backbone with the crystal structure is found near the N-terminus, for residues Asp19-Leu23, which corresponds to an alpha-helix in the crystal structure and to one of the poorest defined regions in the solution structure. To characterize the dynamic behavior of PYP in solution, we undertook a 15N relaxation study and measurements of hydrogen/deuterium exchange. Determination of order parameters through the model-free Lipari-Szabo approach enabled the identification of several regions of enhanced dynamics. The comparison of atomic displacements in the backbone traces of the ensemble structures, with mobility measurements from NMR, show that the poorly defined regions feature fast internal motions in the nanosecond to picosecond time scale.


    Related Citations: 
    • Thiol Ester-Linked P-Coumaric Acid as a New Photoactive Prosthetic Group in a Protein with Rhodopsin-Like Photochemistry
      Hoff, W.D.,Dux, P.,Hard, K.,Devreese, B.,Nugteren-Roodzant, I.M.,Crielaard, W.,Boelens, R.,Kaptein, R.,Van Beeumen, J.,Hellingwerf, K.J.
      (1994) Biochemistry 33: 13959


    Organizational Affiliation

    Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOACTIVE YELLOW PROTEIN
A
125Halorhodospira halophilaGene Names: pyp
Find proteins for P16113 (Halorhodospira halophila)
Go to UniProtKB:  P16113
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HC4
Query on HC4

Download SDF File 
Download CCD File 
A
4'-HYDROXYCINNAMIC ACID
PARA-COUMARIC ACID
C9 H8 O3
NGSWKAQJJWESNS-ZZXKWVIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 26 
  • Selection Criteria: LOW ENERGY 
  • Olderado: 3PHY Olderado
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance