Part:BBa_K091109

LuxS

LuxS is a synthase that produces DPD, which spontaneously forms the AI-2 signaling molecule.

S-ribosylhomocysteine lyase (EC 4.4.1.21) is a metalloenzyme that cleaves the thiol ester bond in RHC and produces homocysteine and DPD, a precursor of AI-2.

Introduction

Vilnius-Lithuania iGEM 2020 project FlavoFlowincludes three goals towards looking for Flavobacterium disease-related problems’ solutions. The project includes creating a rapid detection kit, based on HDA and LFA, developing an implement for treating a disease, and introducing the foundation of edible vaccines. This part was used for the second goal- treatment - of the project FlavoFlow.

Biology

S-ribosylhomocysteine lyase is involved in the synthesis of autoinducer-2 (AI-2), a signaling molecule secreted by bacteria. This phenomenon, when gene expression mechanisms are regulated corresponding to cell density, is called quorum sensing. Mostly regulated genes are involved in antibiotic resistance, biofilm formation, conjugation, swarming processes. The bacterial domain has a way to metabolite/recycle SAH by Pfs and LuxS or SAH-hydrolase¹. Recent studies show that S-ribosylhomocysteinase is coded by the highly conserved luxS gene and is present in the majority of bacteria². LuxS protein catalyzes the transformation of S-ribosyl homocysteine (RHC) to homocysteine (HC) and 4,5-dihydroxy-2,3-pentanedione (DPD).

AI-2 synthesis: S-(5-deoxy-D-ribose-5-yl)-L-homocysteine → (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine

Autoinducer 2 is proposed to be a universal bacterial communication molecule 3 unlike the AI-1, which is species-specific. E. coli has a set of genes called lsr (luxs regulated) which are responsible for uptake and synthesis of AI-2.

The studies of crystal structures show that LuxS exists as a homodimer and has two identical active sites at the dimer interface by residues from both subunits. LuxS active sites contain a divalent metal ion Zn²⁺ or Fe²⁺. The metal ion is tetrahedrally coordinated by the side chains of histidines 54 and 58 in the HXXEH motif and Cys126, and a water molecule. The Fe²⁺ oxidizes the cysteine and causes the modification. This process inactivates the enzyme. The active sites contain Ser6, Phe7, His11, and Arg39 residues. This kind of ligand environment is very similar to that of peptide deformylase. LuxS enzyme like the deformylase loses activity at aerobic conditions due to oxidation³.

Despite that LuxS contains Fe²⁺ ion, tetrahedrally coordinated, S-ribosylhomocysteine‘s ion can be substituted by Co²⁺ without any changes in catalytic properties. Co²⁺ as an ion provides a more stable enzyme than native LuxS². Pei and his colleagues proposed a catalytic mechanism of LuxS. It shows that S-ribosyl homocysteine acts as a Lewis acid, expediting the aldose-ketose isomerization steps³.

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  INCOMPATIBLE WITH RFC[21]

  Illegal BamHI site found at 155
  
• 23
  COMPATIBLE WITH RFC[23]
• 25
  INCOMPATIBLE WITH RFC[25]

  Illegal AgeI site found at 253
  
• 1000
  COMPATIBLE WITH RFC[1000]

References

1. Sun, J., Daniel, R., Wagner-Döbler, I. & Zeng, A.-P. Is autoinducer-2 a universal signal for interspecies communication: a comparative genomic and phylogenetic analysis of the synthesis and signal transduction pathways. BMC Evol Biol 4, 36 (2004).
2. Shen, G., Rajan, R., Zhu, J., Bell, C. E. & Pei, D. Design and Synthesis of Substrate and Intermediate Analogue Inhibitors of S -Ribosylhomocysteinase ‡. J. Med. Chem. 49, 3003–3011 (2006).
3. Pei, D. & Zhu, J. Mechanism of action of S-ribosylhomocysteinase (LuxS). Current Opinion in Chemical Biology 8, 492–497 (2004).