5ZKL

Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7-79) in complex with single-stranded DNA dT12

Summary for 5ZKL

• Entry DOI: 10.2210/pdb5zkl/pdb
• Descriptor: SP_0782, DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') (3 entities in total)
• Functional Keywords: protein-dna complex, unknown function-dna complex, unknown function/dna
• Biological source: Streptococcus pneumoniae R6; More
• Total number of polymer chains: 2
• Total formula weight: 13198.15

Authors

Lu, G.,Li, S.,Zhu, J.,Yang, Y.,Gong, P. (deposition date: 2018-03-24, release date: 2019-03-27, Last modification date: 2023-11-22)

Primary citation

Li, S.,Lu, G.,Fang, X.,Ramelot, T.A.,Kennedy, M.A.,Zhou, X.,Gong, P.,Zhang, X.,Liu, M.,Zhu, J.,Yang, Y.
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.
Nucleic Acids Res., 48:432-444, 2020

PubMed 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.

PubMed: 31713614
DOI: 10.1093/nar/gkz1045

Experimental method

X-RAY DIFFRACTION (1.951 Å)