7N99

SDE2 SAP domain apo structure

Summary for 7N99

• Entry DOI: 10.2210/pdb7n99/pdb
• NMR Information: BMRB: 30927
• Descriptor: Isoform 2 of Replication stress response regulator SDE2 (1 entity in total)
• Functional Keywords: sap domain, sde2, replication stress response regulator, dna binding protein, ssdna binding protein, apo
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 8294.90

Authors

Paung, Y.,Weinheimer, A.S.,Rageul, J.,Khan, A.,Ho, B.,Tong, M.,Alphonse, S.,Seeliger, M.A.,Kim, H. (deposition date: 2021-06-17, release date: 2022-10-12, Last modification date: 2024-05-15)

Primary citation

Weinheimer, A.S.,Paung, Y.,Rageul, J.,Khan, A.,Lo, N.,Ho, B.,Tong, M.,Alphonse, S.,Seeliger, M.A.,Kim, H.
Extended DNA-binding interfaces beyond the canonical SAP domain contribute to the function of replication stress regulator SDE2 at DNA replication forks.
J.Biol.Chem., 298:102268-102268, 2022

PubMed Abstract: Elevated DNA replication stress causes instability of the DNA replication fork and increased DNA mutations, which underlies tumorigenesis. The DNA replication stress regulator silencing-defective 2 (SDE2) is known to bind to TIMELESS (TIM), a protein of the fork protection complex, and enhances its stability, thereby supporting replisome activity at DNA replication forks. However, the DNA-binding activity of SDE2 is not well defined. Here, we structurally and functionally characterize a new conserved DNA-binding motif related to the SAP (SAF-A/B, Acinus, PIAS) domain in human SDE2 and establish its preference for ssDNA. Our NMR solution structure of the SDE2 domain reveals a helix-extended loop-helix core with the helices aligned parallel to each other, consistent with known canonical SAP folds. Notably, we have shown that the DNA interaction of this SAP domain extends beyond the core SAP domain and is augmented by two lysine residues in the C-terminal tail, which is uniquely positioned adjacent to the SAP motif and conserved in the pre-mRNA splicing factor SF3A3. Furthermore, we found that mutation in the SAP domain and extended C terminus not only disrupts ssDNA binding but also impairs TIM localization at replication forks, thus inhibiting efficient fork progression. Taken together, our results establish SDE2 as an essential element for SDE2 to exert its role in preserving replication fork integrity via fork protection complex regulation and highlight the structural diversity of the DNA-protein interactions achieved by a specialized DNA-binding motif.

PubMed: 35850305
DOI: 10.1016/j.jbc.2022.102268

Experimental method

SOLUTION NMR