5KHD

Structure of 1.75 A BldD C-domain-c-di-GMP complex

Summary for 5KHD

• Entry DOI: 10.2210/pdb5khd/pdb
• Descriptor: DNA-binding protein, 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) (3 entities in total)
• Functional Keywords: bldd, streptomyces, c-di-gmp, dna binding protein
• Biological source: Streptomyces venezuelae
• Total number of polymer chains: 2
• Total formula weight: 23076.42

Authors

Schumacher, M. (deposition date: 2016-06-14, release date: 2016-06-29, Last modification date: 2024-03-06)

Primary citation

Tschowri, N.,Schumacher, M.A.,Schlimpert, S.,Chinnam, N.B.,Findlay, K.C.,Brennan, R.G.,Buttner, M.J.
Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development.
Cell, 158:1136-1147, 2014

PubMed Abstract: The cyclic dinucleotide c-di-GMP is a signaling molecule with diverse functions in cellular physiology. Here, we report that c-di-GMP can assemble into a tetramer that mediates the effective dimerization of a transcription factor, BldD, which controls the progression of multicellular differentiation in sporulating actinomycete bacteria. BldD represses expression of sporulation genes during vegetative growth in a manner that depends on c-di-GMP-mediated dimerization. Structural and biochemical analyses show that tetrameric c-di-GMP links two subunits of BldD through their C-terminal domains, which are otherwise separated by ~10 Å and thus cannot effect dimerization directly. Binding of the c-di-GMP tetramer by BldD is selective and requires a bipartite RXD-X8-RXXD signature. The findings indicate a unique mechanism of protein dimerization and the ability of nucleotide signaling molecules to assume alternative oligomeric states to effect different functions.

PubMed: 25171413
DOI: 10.1016/j.cell.2014.07.022

Experimental method

X-RAY DIFFRACTION (1.7501 Å)