The effect of phosphate ion on the ssDNA binding mode of MoSub1, a Sub1/PC4 homolog from rice blast fungus

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.

The large family of PC4-like domains – similar folds and functions throughout all kingdoms of life

“…Similar modes of multimerization-driven unwinding have also been proposed for other ssDNA-binding proteins [67]. The MoSub1 ortholog from rice blast fungus shows another mode of nucleic acid binding (PDB ID: 5zg9) [65]. Here, the dT 19 G ssDNA is bound between two MoSub1 dimers, thereby connecting them (Fig.…”

“… DNA/RNA binding by type II PC4-like fold proteins. The coordinates are taken from: (A) hs PC4 CTD in complex with ssDNA (U mode; PDB ID: 2c62) [ 64 ], (B) Pyricularia oryzae MoSub1 in complex with ssDNA (Straight mode; PDB ID: 4bhm) [ 66 ], (C) Magnaporthe oryzae MoSub1 in complex with ssDNA (L mode; PDB ID: 5zg9) [ 65 ], (D) Lactococcus lactis Ydbc in complex with ssDNA (PDB ID: 2ltt) [ 37 ], (E) Streptococcus pneumonia SP_0782 protein in complex with ssDNA dT12 (PDB ID: 5zkl) [ 39 ], (F) Pseudomonas phage protein PP7 in complex with RNA (PDB ID: 2qux) [ 22 ]. The figure has been prepared in PyMol v 1.3 (pymol.org).…”

Extended DNA-binding interfaces beyond the canonical SAP domain contribute to the function of replication stress regulator SDE2 at DNA replication forks

“…The model of the extended SDE2 SAP domain that has the lowest energy and most Ramachandran favored regions among the 20 best models was chosen as a receptor protein. The ligand ssDNA used was obtained from the crystal structure of MoSub1–ssDNA complex (PDB ID: 5ZG9 ) ( 61 ). One hundred simulation models of SDE2 SAP bound to ssDNA were generated by the HDOCK webserver ( 62 , 63 ) using the template-based docking method.…”

The Role of S. cerevisiae Sub1/PC4 in Transcription Elongation Depends on the C-Terminal Region and Is Independent of the ssDNA Binding Domain

“…In addition, PC4/Sub1 orthologs have been identified in prokaryotes such as in Lactococcus lactis [ 10 ], Burkholderia pseudomallei [ 11 ], and even in the bacteriophage T5 [ 12 ]. It is also pertinent to note that structures of the DNA binding domains of PC4 [ 13 , 14 , 15 ], MoSub1 [ 7 , 9 , 16 ], L. lactis, and bacteriophage T5 have been elucidated. In the case of PC4, it forms homodimers interacting with a 5-nucleotide region of two opposing DNA strands [ 13 , 14 , 17 ].…”