7C4D

Marine microorganism esterase

Summary for 7C4D

• Entry DOI: 10.2210/pdb7c4d/pdb
• Descriptor: Putative esterase, 1,2-ETHANEDIOL, ACETATE ION, ... (5 entities in total)
• Functional Keywords: hydrolase
• Biological source: uncultured bacterium
• Total number of polymer chains: 1
• Total formula weight: 30925.47

Authors

Zhu, C.H.,Wu, Y.K.,Isupov, M.N. (deposition date: 2020-05-16, release date: 2021-05-26, Last modification date: 2023-11-29)

Primary citation

Zhu, C.,Chen, Y.,Isupov, M.N.,Littlechild, J.A.,Sun, L.,Liu, X.,Wang, Q.,Gong, H.,Dong, P.,Zhang, N.,Wu, Y.
Structural Insights into a Novel Esterase from the East Pacific Rise and Its Improved Thermostability by a Semirational Design.
J.Agric.Food Chem., 69:1079-1090, 2021

PubMed Abstract: Lipolytic enzymes are essential biocatalysts in food processing as well as pharmaceutical and pesticide industries, catalyzing the cleavage of ester bonds in a variety of acyl chain substrates. Here, we report the crystal structure of an esterase from the deep-sea hydrothermal vent of the East Pacific Rise (EprEst). The X-ray structure of EprEst in complex with the ligand, acetate, has been determined at 2.03 Å resolution. The structure reveals a unique spatial arrangement and orientation of the helix cap domain and α/β hydrolase domain, which form a substrate pocket with preference for short-chain acyl groups. Molecular docking analysis further demonstrated that the active site pocket could accommodate -nitrophenyl (NP) carboxyl ligands of varying lengths (≤6 C atoms), with NP-butyrate ester predicted to have the highest binding affinity. Additionally, the semirational design was conducted to improve the thermostability of EprEst by enzyme engineering based on the established structure and multiple sequence alignment. A mutation, K114P, introduced in the hinge region of the esterase, which displayed increased thermostability and enzyme activity. Collectively, the structural and functional data obtained herein could be used as basis for further protein engineering to ultimately expand the scope of industrial applications of marine-derived lipolytic enzymes.

PubMed: 33445864
DOI: 10.1021/acs.jafc.0c06338

Experimental method

X-RAY DIFFRACTION (2.03 Å)