The crystal structure of the R52Q mutant demonstrates a role for R52 in chromophore pKa regulation in photoactive yellow protein

Biochemistry
Nobutaka ShimizuM Kataoka

Abstract

Mutating arginine 52 to glutamine (R52Q) in photoactive yellow protein (PYP) increases the pK(a) of the chromophore by 1 pH unit. The structure of the R52Q PYP mutant was determined by X-ray crystallography and was compared to the structure of wild-type PYP to assess the role of R52 in pK(a) regulation. The essential differences between R52Q and the wild type were confined to the loop region containing the 52nd residue. While the hydrogen bonds involving the chromophore were unchanged by the mutation, removing the guanidino group generated a cavity near the chromophore; this cavity is occupied by two water molecules. In the wild type, R52 forms hydrogen bonds with T50 and Y98; these hydrogen bonds are lost in R52Q. Q52 is linked to Y98 by hydrogen bonding through the two water molecules. R52 acts as a lid on the chromophore binding pocket and controls the accessibility of the exterior solvent and the pK(a) of the chromophore. R52 is found to flip out during the formation of PYP(M). The result of this movement is quite similar to the altered structure of R52Q. Thus, we propose that conformational changes at R52 are partly responsible for pK(a) regulation during the photocycle.

Citations

Sep 6, 2013·Journal of the American Chemical Society·Lucille MendonçaYasushi Imamoto
Apr 11, 2008·Photochemistry and Photobiology·Yasushi ImamotoMikio Kataoka
Nov 26, 2015·The Journal of Physical Chemistry. B·Koichi Tamura, Shigehiko Hayashi
Jan 30, 2008·Biophysical Journal·Yasushi ImamotoMikio Kataoka
Dec 24, 2014·The FEBS Journal·Haik ChosrowjanFumio Tanaka
Aug 31, 2006·Photochemistry and Photobiology·Yasushi Imamoto, Mikio Kataoka
Aug 2, 2006·Photochemistry and Photobiology·Tomokazu MorishitaYasushi Imamoto
Aug 15, 2018·Proceedings of the National Academy of Sciences of the United States of America·Shojiro HaraguchiMasashi Unno
Mar 29, 2013·The Journal of Physical Chemistry. B·Jun LiuTakayoshi Kobayashi
Feb 26, 2008·Journal of the American Chemical Society·Gerrit GroenhofMichael A Robb

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