Crystal structure of SSB complexed with inhibitor myricetin

Biochem Biophys Res Commun. 2018 Oct 12;504(4):704-708. doi: 10.1016/j.bbrc.2018.08.188. Epub 2018 Sep 11.


Single-stranded DNA-binding protein (SSB) is essential for all DNA-dependent cellular processes. SSB inhibitors have been recently suggested as broad-spectrum antibacterial agents in antibiotic development. In this paper, we report the first inhibitor-complexed crystal structure of SSB from Pseudomonas aeruginosa PAO1 (PaSSB) at 2.68 Å resolution (PDB entry 5YUN). The inhibitor, myricetin, is a flavonol that possesses many pharmacological activities, such as anticancer, anti-inflammatory, and antibacterial properties, and is beneficial for humans. Four monomers of PaSSB and two of myricetins were found per asymmetric unit. Various interactions between myricetin and PaSSB were examined. Among these, four residues in PaSSB, Lys7, Arg62, Glu80, and Gly107 were found crucial for forming hydrogen bond to myricetin. These two myricetins occupy the grooves for ssDNA-binding of SSB that may prevent ssDNA-wrapping and ssDNA-binding stably from SSB. In addition to explaining how SSB can be inhibited, the myricetin-SSB interaction modes in this paper may also provide insights into how myricetin can bind and inhibit proteins on cancer-signaling pathways.

Keywords: Antibiotics; Myricetin; SSB; SsbA; SsbB; SsbC.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / chemistry
  • Amino Acids / metabolism
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism*
  • Crystallography, X-Ray
  • DNA, Single-Stranded / chemistry
  • DNA, Single-Stranded / metabolism
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism*
  • Flavonoids / chemistry
  • Flavonoids / metabolism*
  • Hydrogen Bonding
  • Molecular Structure
  • Protein Binding
  • Protein Conformation
  • Pseudomonas aeruginosa / metabolism*
  • Static Electricity


  • Amino Acids
  • Bacterial Proteins
  • DNA, Single-Stranded
  • DNA-Binding Proteins
  • Flavonoids
  • myricetin