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Articles

Molecular dynamics study of functionally relevant interdomain and active site interactions in the autotransporter esterase EstA from Pseudomonas aeruginosa

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Pages 743-756 | Received 26 Oct 2019, Accepted 12 May 2020, Published online: 29 May 2020
 

ABSTRACT

Structural and dynamical properties of the autotransporter esterase EstA from bacterium Pseudomonas aeruginosa were studied using molecular dynamics (MD) simulations. Four different systems, including the full-length EstA enzyme inserted into a solvated 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) lipid bilayer, as well as the solvated isolated passenger domain of EstA were simulated without ligand and in complex with 4-hydroxyphenyloctanoate bound as tetrahedral intermediate. Detailed analysis of non-covalent interactions was performed based on 100 ns long MD simulations. It was found that active site interactions include not only the catalytic triad (Ser14, Asp286, His289), but also a three-residue oxyanion hole (backbone of Ser14, Gly92 and Asn147), hydrophobic residues involved in tetrahedral intermediate stabilisation, and residues participating in the active site hydrogen bond network. Moreover, interactions between protein domains were analysed and it was found that interacting residues are located on specific structures not usually found in GDSL hydrolases or autotransporter β barrels. In the case of full-length EstA enzyme, MD simulations point to specific interactions between the central and remote regions of the active site which are important for adequate intermediate stabilisation.

Acknowledgements

We acknowledge bilateral project between Croatia and Germany ‘Biocatalysis of bacterial hydrolases of the GDSL–superfamily studied by a multidisciplinary approach'. We are grateful to Dr. Biserka Kojić-Prodić from RuđerBošković Institute in Zagreb, as well as to Professor Karl-Erich Jaeger and Dr. Filip Kovačić from Forschungszentrum Jülich for valuble disscussions.

Disclosure statement

No potential conflict of interest was reported by the author(s).

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