Short hydrogen bonds in photoactive yellow protein

Eight high-resolution crystal structures of the ground state of photoactive yellow protein (PYP) solved under a variety of conditions reveal that its chromophore is stabilized by two unusually short hydrogen bonds. Both Tyr42 O^η and Glu46 O^ε are separated from the chromophore phenolate oxygen by less than the sum of their atomic van der Waals radii, 2.6 Å. This is characteristic of strong hydrogen bonding, in which hydrogen bonds acquire significant covalent character. The hydrogen bond from the protonated Glu46 to the negatively charged phenolate oxygen is 2.58 ± 0.01 Å in length, while that from Tyr42 is considerably shorter, 2.49 ± 0.01 Å. The E46Q mutant was solved to 0.95 Å resolution; the isosteric mutation increased the length of the hydrogen bond from Glx46 to the chromophore by 0.29 ± 0.01 Å to that of an average hydrogen bond, 2.88 ± 0.01 Å. The very short hydrogen bond from Tyr42 explains why mutating this residue has such a severe effect on the ground-state structure and PYP photocycle. The effect of isosteric mutations on the photocycle can be largely explained by the alterations to the length and strength of these hydrogen bonds.