6MKT

Photoactive Yellow Protein with 3-chlorotyrosine substituted at position 42

Summary for 6MKT

• Entry DOI: 10.2210/pdb6mkt/pdb
• Descriptor: Photoactive yellow protein, 4'-HYDROXYCINNAMIC ACID (3 entities in total)
• Functional Keywords: chlorinated chromophore, hydrogen bonding network, active site, low-barrier hydrogen bond, signaling protein
• Biological source: Halorhodospira halophila
• Total number of polymer chains: 1
• Total formula weight: 14087.18

Authors

Thomson, B.D.,Both, J.,Wu, Y.,Parrish, R.M.,Martinez, T.,Boxer, S.G. (deposition date: 2018-09-26, release date: 2019-05-29, Last modification date: 2023-10-11)

Primary citation

Thomson, B.,Both, J.,Wu, Y.,Parrish, R.M.,Martinez, T.J.,Boxer, S.G.
Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation.
J.Phys.Chem.B, 123:4844-4849, 2019

PubMed Abstract: Photoactive yellow protein (PYP) is a small photoreceptor protein that has two unusually short hydrogen bonds between the deprotonated p-coumaric acid chromophore and two amino acids, a tyrosine and a glutamic acid. This has led to considerable debate as to whether the glutamic acid-chromophore hydrogen bond is a low barrier hydrogen bond, with conflicting results in the literature. We have modified the p K of the tyrosine by amber suppression and of the chromophore by chemical substitution. X-ray crystal structures of these modified proteins are nearly identical to the wild-type protein, so the heavy atom distance between proton donor and acceptor is maintained, even though these modifications change the relative proton affinity between donor and acceptor. Despite a considerable change in relative proton affinity, the NMR chemical shifts of the hydrogen-bonded protons are only moderately affected. QM/MM calculations were used to explore the protons' potential energy surface and connect the calculated proton position with empirically measured proton chemical shifts. The results are inconsistent with a low barrier hydrogen bond but in all cases are consistent with a localized proton, suggesting an ionic hydrogen bond rather than a low barrier hydrogen bond.

PubMed: 31117606
DOI: 10.1021/acs.jpcb.9b01571

Experimental method

X-RAY DIFFRACTION (1.6 Å)