Characterization of transport proteins for aromatic compounds derived from lignin: benzoate derivative binding proteins

J Mol Biol. 2012 Nov 2;423(4):555-75. doi: 10.1016/j.jmb.2012.08.017. Epub 2012 Aug 25.

Abstract

In vitro growth experiments have demonstrated that aromatic compounds derived from lignin can be metabolized and represent a major carbon resource for many soil bacteria. However, the proteins that mediate the movement of these metabolites across the cell membrane have not been thoroughly characterized. To address this deficiency, we used a library representative of lignin degradation products and a thermal stability screen to determine ligand specificity for a set of solute-binding proteins (SBPs) from ATP-binding cassette (ABC) transporters. The ligand mapping process identified a set of proteins from Alphaproteobacteria that recognize various benzoate derivatives. Seven high-resolution crystal structures of these proteins in complex with four different aromatic compounds were obtained. The protein-ligand complexes provide details of molecular recognition that can be used to infer binding specificity. This structure-function characterization provides new insight for the biological roles of these ABC transporters and their SBPs, which had been previously annotated as branched-chain amino-acid-binding proteins. The knowledge derived from the crystal structures provides a foundation for development of sequence-based methods to predict the ligand specificity of other uncharacterized transporters. These results also demonstrate that Alphaproteobacteria possess a diverse set of transport capabilities for lignin-derived compounds. Characterization of this new class of transporters improves genomic annotation projects and provides insight into the metabolic potential of soil bacteria.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • ATP-Binding Cassette Transporters / chemistry*
  • ATP-Binding Cassette Transporters / metabolism*
  • Alphaproteobacteria / metabolism
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism
  • Benzoates / metabolism*
  • Binding Sites
  • Biological Transport, Active*
  • Cell Membrane / enzymology
  • Cell Membrane / metabolism*
  • Crystallography, X-Ray
  • Ligands
  • Lignin
  • Protein Binding
  • Protein Folding
  • Protein Structure, Tertiary
  • Structure-Activity Relationship

Substances

  • ATP-Binding Cassette Transporters
  • Bacterial Proteins
  • Benzoates
  • Ligands
  • Lignin

Associated data

  • PDB/4EVQ
  • PDB/4EVR
  • PDB/4EVS
  • PDB/4EY3
  • PDB/4EYG
  • PDB/4EYK
  • PDB/4F06