2ZOI

Neutron Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.192 

wwPDB Validation

Currently 2ZOI does not have a wwPDB validation report.


This is version 1.1 of the entry. See complete history

Literature

Low-barrier hydrogen bond in photoactive yellow protein

Yamaguchi, S.Kamikubo, H.Kurihara, K.Kuroki, R.Niimura, N.Shimizu, N.Yamazaki, Y.Kataoka, M.

(2009) Proc.Natl.Acad.Sci.USA 106: 440-444

  • DOI: 10.1073/pnas.0811882106
  • Primary Citation of Related Structures:  2ZOH

  • PubMed Abstract: 
  • 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 expe ...

    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.


    Organizational Affiliation

    Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.




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 2 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
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.192 
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
MACSCIENCEdata collection

Structure Validation

Currently 2ZOI does not have a wwPDB validation report.



Entry History 

Deposition Data

  • Deposited Date: 2008-05-21 
  • Released Date: 2009-03-24 
  • Deposition Author(s): Yamaguchi, S.

Revision History 

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance