The enthalpy and structural volume changes (ΔH_i and ΔV_i) produced upon photoinduced formation and decay of the red-shifted intermediate (pR = I₁) in the photoactive yellow protein (WT-PYP) from Halorhodospira halophila and the mutated E46Q-PYP and E46A-PYP, were determined by laser-induced optoacoustic spectroscopy (LIOAS) using the two-temperatures method, at pH 8.5. These mutations alter the hydrogen bond between the phenolate oxygen of the chromophore and the residue at position 46. Hydrogen bonding is still possible in E46Q-PYP via the δ-NH₂ group of glutamine, whereas it is no longer possible with the methyl group of alanine in E46A-PYP. In all three proteins, pR decays within hundreds of ns to µs into the next intermediate, pR′. The ΔH values for the formation of pR (ΔH_pR) and for its decay into pR′(ΔH_pR→pR′) are negligibly affected by the E46Q and the E46A substitution. In all three proteins the large ΔH_pR value drives the photocycle. Whereas ΔV_pR is a similar contraction of ca. 15 ml mol⁻¹ for E46Q-PYP and WT-PYP, attributed to strengthening the hydrogen bond network (between 4 and 5 hydrogen bonds) inside the protein chromophore cavity, an expansion is observed for E46A-PYP, indicating just an enlargement of the chromophore cavity upon chromophore isomerization. The results are discussed in the light of the recent time-resolved room temperature, crystallographic studies with WT-PYP and E46Q-PYP. Formation of pR′ is somewhat slower for E46Q-PYP and much slower for E46A-PYP. The structural volume change for this transition, ΔV_pR→pR′, is relatively small and positive for WT-PYP, slightly larger for E46Q-PYP, and definitely larger for the hydrogen-bond lacking E46A-PYP. This indicates a larger entropic change for this transition in E46A-PYP, reflected in the large pre-exponential factor for the pR to pR′ decay rate constant determined in the 5–30 °C temperature range. This decay also shows an activation entropy that compensates the larger activation energy in E46A-PYP, as compared to the values for WT-PYP and E46Q-PYP.