1. Structural insight into the length-dependent binding of ssDNA by SP_0782 from Streptococcus pneumoniae, reveals a divergence in the DNA-binding interface of PC4-like proteins
- Author
-
Guoliang Lu, Xu Zhang, Xin Zhou, Jiang Zhu, Maili Liu, Shuangli Li, Yunhuang Yang, Peng Gong, M.A. Kennedy, Xiang Fang, and Theresa Ramelot
- Subjects
DNA, Bacterial ,Models, Molecular ,Protein Conformation, alpha-Helical ,Protein Folding ,Beta sheet ,DNA, Single-Stranded ,Plasma protein binding ,Biology ,Crystallography, X-Ray ,03 medical and health sciences ,chemistry.chemical_compound ,Protein structure ,Bacterial Proteins ,Structural Biology ,Transcription (biology) ,Genetics ,Humans ,Protein Interaction Domains and Motifs ,Nucleotide ,Binding site ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Binding Sites ,030302 biochemistry & molecular biology ,DNA-Binding Proteins ,Lactococcus lactis ,Kinetics ,Streptococcus pneumoniae ,chemistry ,Biophysics ,Nucleic Acid Conformation ,Thermodynamics ,Protein Conformation, beta-Strand ,Protein folding ,DNA ,Protein Binding ,Transcription Factors - Abstract
SP_0782 from Streptococcus pneumoniae is a dimeric protein that potentially binds with single-stranded DNA (ssDNA) in a manner similar to human PC4, the prototype of PC4-like proteins, which plays roles in transcription and maintenance of genome stability. In a previous NMR study, SP_0782 exhibited an ssDNA-binding property different from YdbC, a prokaryotic PC4-like protein from Lactococcus lactis, but the underlying mechanism remains unclear. Here, we show that although SP_0782 adopts an overall fold similar to those of PC4 and YdbC, the ssDNA length occupied by SP_0782 is shorter than those occupied by PC4 and YdbC. SP_0782 exhibits varied binding patterns for different lengths of ssDNA, and tends to form large complexes with ssDNA in a potential high-density binding manner. The structures of SP_0782 complexed with different ssDNAs reveal that the varied binding patterns are associated with distinct capture of nucleotides in two major DNA-binding regions of SP_0782. Moreover, a comparison of known structures of PC4-like proteins complexed with ssDNA reveals a divergence in the binding interface between prokaryotic and eukaryotic PC4-like proteins. This study provides insights into the ssDNA-binding mechanism of PC4-like proteins, and benefits further study regarding the biological function of SP_0782, probably in DNA protection and natural transformation.
- Published
- 2019