8U8M

X-ray crystal structure of TEBP-1 MCD2 homodimer

Summary for 8U8M

• Entry DOI: 10.2210/pdb8u8m/pdb
• Descriptor: Double-strand telomeric DNA-binding proteins 1, COBALT (II) ION (3 entities in total)
• Functional Keywords: telomeres, c. elegans, shelterin, dna-binding protein, tebp-1, dtn-1, homodimerization, myb, homeodomain, protein binding
• Biological source: Caenorhabditis elegans
• Total number of polymer chains: 4
• Total formula weight: 54946.20

Authors

Nandakumar, J.,Padmanaban, S. (deposition date: 2023-09-18, release date: 2024-04-03, Last modification date: 2024-04-24)

Primary citation

Padmanaban, S.,Lambacher, N.J.,Tesmer, V.M.,Zhang, J.,Shibuya, H.,Nandakumar, J.
Caenorhabditis elegans telomere-binding proteins TEBP-1 and TEBP-2 adapt the Myb module to dimerize and bind telomeric DNA.
Proc.Natl.Acad.Sci.USA, 121:e2316651121-e2316651121, 2024

PubMed Abstract: Protecting chromosome ends from misrecognition as double-stranded (ds) DNA breaks is fundamental to eukaryotic viability. The protein complex shelterin prevents a DNA damage response at mammalian telomeres. Mammalian shelterin proteins TRF1 and TRF2 and their homologs in yeast and protozoa protect telomeric dsDNA. N-terminal homodimerization and C-terminal Myb-domain-mediated dsDNA binding are two structural hallmarks of end protection by TRF homologs. Yet our understanding of how protects its telomeric dsDNA is limited. Recently identified proteins TEBP-1 (also called DTN-1) and TEBP-2 (also called DTN-2) are functional homologs of TRF proteins, but how they bind DNA and whether or how they dimerize is not known. TEBP-1 and TEBP-2 harbor three Myb-containing domains (MCDs) and no obvious dimerization domain. We demonstrate biochemically that only the third MCD binds DNA. We solve the X-ray crystal structure of TEBP-2 MCD3 with telomeric dsDNA to reveal the structural mechanism of telomeric dsDNA protection in . Mutagenesis of the DNA-binding site of TEBP-1 and TEBP-2 compromises DNA binding in vitro, and increases DNA damage signaling, lengthens telomeres, and decreases brood size in vivo. Via an X-ray crystal structure, biochemical validation of the dimerization interface, and SEC-MALS analysis, we demonstrate that MCD1 and MCD2 form a composite dimerization module that facilitates not only TEBP-1 and TEBP-2 homodimerization but also heterodimerization. These findings provide fundamental insights into telomeric dsDNA protection and highlight how different eukaryotes have evolved distinct strategies to solve the chromosome end protection problem.

PubMed: 38588418
DOI: 10.1073/pnas.2316651121

Experimental method

X-RAY DIFFRACTION (2.7 Å)