PDBsum entry 6mhn

Signaling protein

PDB id: 6mhn

Contents

Protein chain

125 a.a.

Ligands

YAZ

Waters ×91

PDB id:

6mhn

Name:

Signaling protein

Title:

Photoactive yellow protein with covalently bound 3-chloro-4- hydroxycinnamic acid chromophore

Structure:

Photoactive yellow protein. Chain: a. Synonym: pyp. Engineered: yes

Source:

Halorhodospira halophila. Organism_taxid: 1053. Gene: pyp. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.67Å R-factor: 0.172 R-free: 0.215

Authors:

B.D.Thomson,J.Both,Y.Wu,R.M.Parrish,T.Martinez,S.G.Boxer

Key ref:

B.Thomson et al. (2019). Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation. J Phys Chem B, 123, 4844-4849. PubMed id: 31117606 DOI: 10.1021/acs.jpcb.9b01571

Date:

18-Sep-18 Release date: 29-May-19

Protein chain

P16113  (PYP_HALHA) -  Photoactive yellow protein from Halorhodospira halophila

Seq: 125 a.a.

Struc: 125 a.a.

DOI no: 10.1021/acs.jpcb.9b01571

J Phys Chem B 123:4844-4849 (2019)

PubMed id: 31117606

Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation.

B.Thomson, J.Both, Y.Wu, R.M.Parrish, T.J.Martínez, S.G.Boxer.

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_a 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.