We have investigated primary processes of ultrafast photoreactions of various photoresponsive proteins by means of fs fluorescence dynamics measurements. Based on these studies, the effects of the protein nanospace (PNS), containing the chromophore, on the dynamics and mechanisms of the ultrafast and highly efficient reactions of these proteins have been elucidated. In this article, we discuss mainly the results of our studies on ultrafast photoisomerization of photoactive yellow protein (PYP), its mutants and analogues. The chromophore of the PYP, deprotonated coumaric acid thioester (O⁻-phenyl-CHCH–CO–S–CH₂–), fixed in PNS by hydrogen (H) bonding interactions at the head part, O⁻-phenyl-, and by covalent bonding at the tail part, –CO–S–, undergoes ultrafast twisting by flipping the thioester bond, owing to the intrachromophore head to tail charge transfer caused by the photoexcitation. In the site-directed mutants where the PNS structure is looser and more disordered, the photoinduced twisting reaction becomes slowed compared with the wild-type PYP and moreover, the twisting becomes much slower in the denatured PYP, showing the supreme importance of more regulated PNS for the fast twisting. We found also coherent vibrations in the fluorescence decay curves which might be coupled with the twisting. Furthermore, we found for a PYP analogue with replaced chromophore ultrafast dynamic Stokes shift of fluorescence rather than the quenching due to twisting, indicating the importance of chromophore-PNS fine adjustment for the ultrafast twisting.