9DZM

Dimeric human OCT2 (POU2F2) POU domain bound to palindromic MORE DNA

Summary for 9DZM

• Entry DOI: 10.2210/pdb9dzm/pdb
• Descriptor: DNA (5'-D(*TP*CP*CP*TP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*AP*GP*G)-3'), DNA (5'-D(*TP*CP*CP*TP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*A)-3'), POU domain, class 2, transcription factor 2, ... (5 entities in total)
• Functional Keywords: transcription factor, protein-dna complex, transcription-dna complex, transcription, transcription/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 6
• Total formula weight: 90381.83

Authors

Terrell, J.R.,Poon, G.M.K. (deposition date: 2024-10-16, release date: 2024-10-23, Last modification date: 2025-03-12)

Primary citation

Terrell, J.R.,Poon, G.M.K.
Coupled Heterogeneity to Dimeric Site-Specific Binding by the POU-Family Transcription Factor OCT2.
J.Phys.Chem.B, 129:2138-2148, 2025

PubMed Abstract: POU-family transcription factors regulate metazoan gene expression via a bipartite DNA-binding domain consisting of two covalently linked helix-turn-helix subdomains, POU and POU. POU factors bind as dimers to DNA half-sites to form complexes with a variable quaternary structure. To enhance the knowledge of the physical chemistry of dimeric POU/DNA recognition, we carried out a crystallographic and titration analysis of the cooperative homodimer formed by the POU factor OCT2 and an optimized palindromic DNA site known as MORE. The data evidence strong heterogeneity in the binding and formation of secondary complexes in site-specific DNA recognition by OCT2 at thermodynamic equilibrium. These secondary complexes are strictly contingent to the site-specific complex, detectable at subsaturating OCT2 concentrations, and cooperate with nonspecific binding to guide the affinity of the site-specific complex. Modulation with salt and poly[d(I-C)] unmasks the compensation between nonspecific DNA depleting unbound OCT2 on the one hand while driving specific binding by intermolecular transfer of OCT2 via secondary complexes on the other. Molecular dynamics simulations extend a mechanism, previously proposed for POU monomers, in which the two subdomains dynamically cross-link DNA strands to form supramolecular dimeric POU/DNA complexes at equilibrium.

PubMed: 39960871
DOI: 10.1021/acs.jpcb.4c07071

Experimental method

X-RAY DIFFRACTION (2.54 Å)