5TZF

Structure of the BldD CTD(D116A)-(c-di-GMP)2 intermediate, form 1

Summary for 5TZF

• Entry DOI: 10.2210/pdb5tzf/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, c-di-gmp, assembly intermediate, dna binding protein
• Biological source: Streptomyces venezuelae
• Total number of polymer chains: 8
• Total formula weight: 86430.31

Authors

Schumacher, M.A. (deposition date: 2016-11-21, release date: 2017-04-19, Last modification date: 2023-10-04)

Primary citation

Schumacher, M.A.,Zeng, W.,Findlay, K.C.,Buttner, M.J.,Brennan, R.G.,Tschowri, N.
The Streptomyces master regulator BldD binds c-di-GMP sequentially to create a functional BldD2-(c-di-GMP)4 complex.
Nucleic Acids Res., 45:6923-6933, 2017

PubMed Abstract: Streptomyces are ubiquitous soil bacteria that undergo a complex developmental transition coinciding with their production of antibiotics. This transition is controlled by binding of a novel tetrameric form of the second messenger, 3΄-5΄ cyclic diguanylic acid (c-di-GMP) to the master repressor, BldD. In all domains of life, nucleotide-based second messengers allow a rapid integration of external and internal signals into regulatory pathways that control cellular responses to changing conditions. c-di-GMP can assume alternative oligomeric states to effect different functions, binding to effector proteins as monomers, intercalated dimers or, uniquely in the case of BldD, as a tetramer. However, at physiological concentrations c-di-GMP is a monomer and little is known about how higher oligomeric complexes assemble on effector proteins and if intermediates in assembly pathways have regulatory significance. Here, we show that c-di-GMP binds BldD using an ordered, sequential mechanism and that BldD function necessitates the assembly of the BldD2-(c-di-GMP)4 complex.

PubMed: 28449057
DOI: 10.1093/nar/gkx287

Experimental method

X-RAY DIFFRACTION (2.4 Å)