2zoh

From Proteopedia

X-ray Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K

PDB ID 2zoh

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Structural highlights

2zoh is a 1 chain structure with sequence from Halorhodospira halophila. The March 2015 RCSB PDB Molecule of the Month feature on Phototropin by David Goodsell is 10.2210/rcsb_pdb/mom_2015_3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.25Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PYP_HALHA Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

Low-barrier hydrogen bond in photoactive yellow protein.,Yamaguchi S, Kamikubo H, Kurihara K, Kuroki R, Niimura N, Shimizu N, Yamazaki Y, Kataoka M Proc Natl Acad Sci U S A. 2009 Jan 13;106(2):440-4. Epub 2009 Jan 2. PMID:19122140^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Yamaguchi S, Kamikubo H, Kurihara K, Kuroki R, Niimura N, Shimizu N, Yamazaki Y, Kataoka M. Low-barrier hydrogen bond in photoactive yellow protein. Proc Natl Acad Sci U S A. 2009 Jan 13;106(2):440-4. Epub 2009 Jan 2. PMID:19122140