The flexible conformations of a multi-domain protein are responsible for its biological functions. Although MurD, a 47-kDa protein which consists of three domains, sequentially changes its domain conformation from an open form to a closed form through a semi-closed form in its enzymatic reaction, the domain dynamics in each conformation remains unclear. In this study, we verify the conformational dynamics of MurD in the corresponding three states (apo, ATP- and inhibitor-bound states), with a combination of small-angle X-ray and neutron scattering (SAXS and SANS), dynamic light scattering (DLS), neutron backscattering (NBS), neutron spin echo (NSE) spectroscopy and molecular dynamics (MD) simulations. Applying principal component analysis of the MD trajectories, a twisting and an open-closed domain modes are identified as the major collective coordinates. The deviations of the experimental SAXS profiles from the theoretical calculations based on the known crystal structures becomes smaller in the ATP-bound state than in the apo state, and a further decrease is evident upon inhibitor-binding. These results suggest that domain motions of the protein are suppressed step-by-step of each ligand binding. The DLS and NBS data yield collective- and self-translational diffusion constants, respectively, and we used them to extract collective domain motions in nanometer and nanosecond scale from the NSE data. In the apo state, MurD shows both twisting and open-closed domain modes, while an ATP binding suppresses twisting domain motions and a further reduction of open-closed mode is seen in the inhibitor binding state. These observations are consistent with the structure modifications measured by the small-angle scattering as well as the MD simulations. Such changes in the domain dynamics associated with the sequential enzymatic reactions should be related to the affinity and reaction efficiency with a ligand that binds specifically to each reaction state.