2ZOI: Neutron Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K

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.
PDB ID: 2ZOIDownload
MMDB ID: 70344
PDB Deposition Date: 2008/5/21
Updated in MMDB: 2011/10
Experimental Method:
neutron diffraction
Resolution: 1.5  Å
Source Organism:
Similar Structures:
Biological Unit for 2ZOI: monomeric; determined by author and by software (PISA)
Molecular Components in 2ZOI
Label Count Molecule
Protein (1 molecule)
Photoactive Yellow Protein
Molecule annotation
Chemical (1 molecule)
* Click molecule labels to explore molecular sequence information.

Citing MMDB