Crystal structure of chloramphenicol-metabolizing enzyme EstDL136 from a metagenome

PLoS One. 2019 Jan 15;14(1):e0210298. doi: 10.1371/journal.pone.0210298. eCollection 2019.

Abstract

Metagenomes often convey novel biological activities and therefore have gained considerable attention for use in biotechnological applications. Recently, metagenome-derived EstDL136 was found to possess chloramphenicol (Cm)-metabolizing features. Sequence analysis showed EstDL136 to be a member of the hormone-sensitive lipase (HSL) family with an Asp-His-Ser catalytic triad and a notable substrate specificity. In this study, we determined the crystal structures of EstDL136 and in a complex with Cm. Consistent with the high sequence similarity, the structure of EstDL136 is homologous to that of the HSL family. The active site of EstDL136 is a relatively shallow pocket that could accommodate Cm as a substrate as opposed to the long acyl chain substrates typical of the HSL family. Mutational analyses further suggested that several residues in the vicinity of the active site play roles in the Cm-binding of EstDL136. These results provide structural and functional insights into a metagenome-derived EstDL136.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Catalytic Domain / genetics
  • Chloramphenicol / chemistry
  • Chloramphenicol / metabolism*
  • Crystallography, X-Ray
  • Kinetics
  • Metagenome
  • Models, Molecular
  • Mutagenesis
  • Sequence Homology, Amino Acid
  • Soil Microbiology
  • Sterol Esterase / chemistry*
  • Sterol Esterase / genetics
  • Sterol Esterase / metabolism*
  • Substrate Specificity

Substances

  • Chloramphenicol
  • Sterol Esterase

Grants and funding

This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ01325801 to SR), Rural Development Administration of Korea and by the National Research Foundation of Korea grant (2017R1A2B4002860) from MSIP, Republic of Korea (to SR). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.