Download MendeleyDistinct Modes of Hidden Structural Dynamics in the Functioning of an Allosteric Polysaccharide Lyase.
Dash, P., Acharya, R.(2022) ACS Cent Sci 8: 933-947
- PubMed: 35912344
- DOI: https://doi.org/10.1021/acscentsci.2c00277
- Primary Citation of Related Structures:
7WXJ, 7WXK, 7WXL, 7WXM, 7WXN, 7WXO, 7WXP, 7WXQ, 7WXR, 7XTE, 7XTF - PubMed Abstract:
Dynamics is an essential process to drive an enzyme to perform a function. When a protein sequence encodes for its three-dimensional structure and hence its function, it essentially defines the intrinsic dynamics of the molecule. The static X-ray crystal structure was thought to shed little insight into the molecule's dynamics until the recently available tool "Ensemble refinement" (ER). Here, we report the structure-function-dynamics of PanPL, an alginate-specific, endolytic, allosteric polysaccharide lyase belonging to the PL-5 family from Pandoraea apista . The crystal structures determined in apo and tetra-ManA bound forms reveal that the PanPL maintains a closed state with an N-terminal loop lid (N-loop-lid) arched over the active site. The B-factor analyses and ER congruently reveal how pH influences the functionally relevant atomic fluctuations at the N-loop-lid. The ER unveils enhanced fluctuations at the N-loop-lid upon substrate binding. The normal-mode analysis finds that the functional states are confined. The 1 μs simulation study suggests the existence of a hidden open state. The longer N-loop-lid selects a mechanism to adopt a closed state and undergo fluctuations to facilitate the substrate binding. Here, our work demonstrates the distinct modes of dynamics; both intrinsic and substrate-induced conformational changes are vital for enzyme functioning and allostery.
Organizational Affiliation:
School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, 752050, Odisha, India.
