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

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.

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

“…Each structure is depicted in two different orientations. The coordinates are taken from: (A) Solanum tuberosum P24 subunit of PBF-2 (PDB ID: 1l3a) [ 20 ], (B) Trypanosoma brucei MRP1 (PDB ID: 2gje) [ 21 ], (C) The human replication and transcription cofactor PC4 (PDB ID: 1pcf) [ 18 ], (D) Bacteriophage T5 homologue of PC4 (PDB ID: 4bg7) [ 36 ], (E) Lactococcus lactis DUF2128 family member YdbC (PDB ID: 2ltt) [ 37 ], (F) Pur-α from Borrelia burgdorferi (PDB ID: 3n8b) [ 13 ], (G) Streptococcus pneumonia SP_0782 protein (PDB ID: 5zkl) [ 39 ], (H) The bacteriophage coat protein PP7 (PDB ID: 2qux) [ 22 ]. The structures of type I PC4-like fold have been represented as cyan (repeat I) and navy blue (repeat II), whereas in the structures of type II PC4-like fold individual chains have been shown in green and grey.…”

“… 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).…”

“…It is potentially involved in maintenance of genome stability and natural transformation [38]. Its structure has been determined in complex with ssDNA (Northeast Structural Genomics Consortium; PDB ID: 5zkl [39]; Fig. 2G and Supplementary Fig.…”

“…Very recently, DNA binding has been shown also for SP_0782 protein (fragment 7-79) from S. pneumonia. The complex of this protein with single stranded DNA dT12 (Northeast Structural Genomics Consortium; PDB ID: 5zkl [39]) shows a straight mode of DNA binding ( Fig. 5E and Supplementary Fig.…”