7VUM

Crystal structure of SSB complexed with que

This is a non-PDB format compatible entry.

Summary for 7VUM

• Entry DOI: 10.2210/pdb7vum/pdb
• Descriptor: Single-stranded DNA-binding protein, 3,5,7,3',4'-PENTAHYDROXYFLAVONE (3 entities in total)
• Functional Keywords: single-strand dna binding protein, dna binding protein
• Biological source: Pseudomonas aeruginosa PAO1
• Total number of polymer chains: 4
• Total formula weight: 55399.60

Authors

Lin, E.S.,Huang, Y.H.,Huang, C.Y. (deposition date: 2021-11-03, release date: 2022-03-09, Last modification date: 2023-11-29)

Primary citation

Lin, E.S.,Luo, R.H.,Huang, C.Y.
A Complexed Crystal Structure of a Single-Stranded DNA-Binding Protein with Quercetin and the Structural Basis of Flavonol Inhibition Specificity.
Int J Mol Sci, 23:-, 2022

PubMed Abstract: Single-stranded DNA (ssDNA)-binding protein (SSB) plays a crucial role in DNA replication, repair, and recombination as well as replication fork restarts. SSB is essential for cell survival and, thus, is an attractive target for potential antipathogen chemotherapy. Whether naturally occurring products can inhibit SSB remains unknown. In this study, the effect of the flavonols myricetin, quercetin, kaempferol, and galangin on the inhibition of SSB (PaSSB) was investigated. Furthermore, SSB was identified as a novel quercetin-binding protein. Through an electrophoretic mobility shift analysis, myricetin could inhibit the ssDNA binding activity of PaSSB with an IC of 2.8 ± 0.4 μM. The effect of quercetin, kaempferol, and galangin was insignificant. To elucidate the flavonol inhibition specificity, the crystal structure of PaSSB complexed with the non-inhibitor quercetin was solved using the molecular replacement method at a resolution of 2.3 Å (PDB entry 7VUM) and compared with a structure with the inhibitor myricetin (PDB entry 5YUN). Although myricetin and quercetin bound PaSSB at a similar site, their binding poses were different. Compared with myricetin, the aromatic ring of quercetin shifted by a distance of 4.9 Å and an angle of 31 for hydrogen bonding to the side chain of Asn108 in PaSSB. In addition, myricetin occupied and interacted with the ssDNA binding sites Lys7 and Glu80 in PaSSB whereas quercetin did not. This result might explain why myricetin could, but quercetin could not, strongly inhibit PaSSB. This molecular evidence reveals the flavonol inhibition specificity and also extends the interactomes of the natural anticancer products myricetin and quercetin to include the OB-fold protein SSB.

PubMed: 35054774
DOI: 10.3390/ijms23020588

Experimental method

X-RAY DIFFRACTION (2.319 Å)