Molecular mechanism of environmental d-xylose perception by a XylFII-LytS complex in bacteria

Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):8235-8240. doi: 10.1073/pnas.1620183114. Epub 2017 Jul 17.


d-xylose, the main building block of plant biomass, is a pentose sugar that can be used by bacteria as a carbon source for bio-based fuel and chemical production through fermentation. In bacteria, the first step for d-xylose metabolism is signal perception at the membrane. We previously identified a three-component system in Firmicutes bacteria comprising a membrane-associated sensor protein (XylFII), a transmembrane histidine kinase (LytS) for periplasmic d-xylose sensing, and a cytoplasmic response regulator (YesN) that activates the transcription of the target ABC transporter xylFGH genes to promote the uptake of d-xylose. The molecular mechanism underlying signal perception and integration of these processes remains elusive, however. Here we purified the N-terminal periplasmic domain of LytS (LytSN) in a complex with XylFII and determined the conformational structures of the complex in its d-xylose-free and d-xylose-bound forms. LytSN contains a four-helix bundle, and XylFII contains two Rossmann fold-like globular domains with a xylose-binding cleft between them. In the absence of d-xylose, LytSN and XylFII formed a heterodimer. Specific binding of d-xylose to the cleft of XylFII induced a large conformational change that closed the cleft and brought the globular domains closer together. This conformational change led to the formation of an active XylFII-LytSN heterotetramer. Mutations at the d-xylose binding site and the heterotetramer interface diminished heterotetramer formation and impaired the d-xylose-sensing function of XylFII-LytS. Based on these data, we propose a working model of XylFII-LytS that provides a molecular basis for d-xylose utilization and metabolic modification in bacteria.

Keywords: cross-membrane signaling; d-xylose uptake; histidine kinase; molecular mechanism; two-component system.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Binding Sites
  • Cell Membrane / metabolism
  • Clostridium beijerinckii / metabolism*
  • Crystallography, X-Ray
  • Histidine Kinase / metabolism
  • Models, Molecular
  • Multiprotein Complexes
  • Protein Conformation
  • Protein Multimerization
  • Xylose / metabolism*


  • Bacterial Proteins
  • Multiprotein Complexes
  • Xylose
  • Histidine Kinase

Associated data

  • PDB/5XSD
  • PDB/5XSJ
  • PDB/5XSS