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Visualization of H atoms in the X‐ray crystal structure of photoactive yellow protein: Does it contain low‐barrier hydrogen bonds?
Author(s) -
Wang Jimin
Publication year - 2019
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.3716
Subject(s) - crystallography , chemistry , protein data bank (rcsb pdb) , hydrogen bond , protonation , crystal structure , hydrogen atom , deprotonation , molecule , stereochemistry , organic chemistry , ion , alkyl
The hydrogen bond (HB) between 4‐hydroxycinnamic acid (HC4) and glutamic acid E46 of photoactive yellow protein is exceptionally strong. In the 0.82‐å resolution X‐ray structure for this protein (PDB ID: 1NWZ ), the OH…O distance is only 2.57 å. The position of the H atom between these two O atoms has not been determined in that structure, and in the absence of that information, it is impossible to determine whether or not this HB is a low‐barrier HB (LBHB), as was proposed recently based on neutron structures of this protein (Yamaguchi et al., Proceedings of the National Academy of Sciences of the United States of America, 2009, 106: 440–444). Residual electron density maps computed using the 1NWZ data reveal that this H atom is 0.92 å from the O ε2 atom of E46 and 1.67 å from the O 4 ′ of HC4, and that the OH…O bond angle is 167°. These observations indicate that E46 is protonated, and HC4 is deprotonated, as was originally suggested, and that the HB in question is not an LBHB.