SNAP output for PDB entry 5zg9 [SNAP web server]

PDB-id

5zg9; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein-DNA

Method

X-ray (2.04 Å)

Summary

Crystal structure of mosub1-ssDNA complex in phosphate buffer

Reference

Zhao Y, Zhang Y, Huang J, Wang S, Yi L, Zhang X, Xu M, Fang X, Liu J (2019): "The effect of phosphate ion on the ssDNA binding mode of MoSub1, a Sub1/PC4 homolog from rice blast fungus." Proteins, 87, 257-264. doi: 10.1002/prot.25647.

Abstract

MoSub1 is an ortholog of yeast single stranded DNA binding protein Sub1 or human PC4 from rice blast fungus. All of them share a similar DNA binding region and may have similar biological roles. The well-studied Sub1/PC4 has been reported to play multiple roles in DNA metabolic processes, such as transcription and DNA repair and their DNA binding capacity is significantly affected by phosphorylation. Here, we determined the crystal structure of MoSub1 complexed with ssDNA in a phosphate solution. The crystal structure of the MoSub1-ssDNA complex was solved to a resolution of 2.04 Å. A phosphate ion at the interface of the protein-DNA interaction of the complex bridged the lys84 of the protein and two nucleotides. The DNA was bound in novel mode (L mode) in the MoSub1 complex in the presence of phosphate ions, while DNA bound in the straight mode in the absence of the phosphate ion and in U mode in the same binding motif of the PC4-ssDNA complex. The crystal structure of the complex and a small-angle X-ray scattering analysis revealed that the phosphate ion at the protein-DNA interface affected the DNA binding mode of MoSub1 to oligo-DNA and provided a new structural clue for studying its functions.