3E7L

Crystal structure of sigma54 activator NtrC4's DNA binding domain

Summary for 3E7L

• Entry DOI: 10.2210/pdb3e7l/pdb
• Related: 3DZD
• Descriptor: Transcriptional regulator (NtrC family), ZINC ION (3 entities in total)
• Functional Keywords: sigma43 activator, aaa+ atpase, response regulator, transcriptional activator, atp-binding, nucleotide-binding, transcription, transcription regulator
• Biological source: Aquifex aeolicus
• Total number of polymer chains: 4
• Total formula weight: 30933.39

Authors

Batchelor, J.D.,Doucleff, M.,Lee, C.-J.,Matsubara, K.,De Carlo, S.,Heideker, J.,Lamers, M.M.,Pelton, J.G.,Wemmer, D.E. (deposition date: 2008-08-18, release date: 2008-11-25, Last modification date: 2024-02-21)

Primary citation

Batchelor, J.D.,Doucleff, M.,Lee, C.J.,Matsubara, K.,De Carlo, S.,Heideker, J.,Lamers, M.H.,Pelton, J.G.,Wemmer, D.E.
Structure and regulatory mechanism of Aquifex aeolicus NtrC4: variability and evolution in bacterial transcriptional regulation.
J.Mol.Biol., 384:1058-1075, 2008

PubMed Abstract: Genetic changes lead gradually to altered protein function, making deduction of the molecular basis for activity from a sequence difficult. Comparative studies provide insights into the functional consequences of specific changes. Here we present structural and biochemical studies of NtrC4, a sigma-54 activator from Aquifex aeolicus, and compare it with NtrC1 (a paralog) and NtrC (a homolog from Salmonella enterica) to provide insight into how a substantial change in regulatory mechanism may have occurred. Activity assays show that assembly of NtrC4's active oligomer is repressed by the N-terminal receiver domain, and that BeF3- addition (mimicking phosphorylation) removes this repression. Observation of assembly without activation for NtrC4 indicates that it is much less strongly repressed than NtrC1. The crystal structure of the unactivated receiver-ATPase domain combination shows a partially disrupted interface. NMR structures of the regulatory domain show that its activation mechanism is very similar to that of NtrC1. The crystal structure of the NtrC4 DNA-binding domain shows that it is dimeric and more similar in structure to NtrC than NtrC1. Electron microscope images of the ATPase-DNA-binding domain combination show formation of oligomeric rings. Sequence alignments provide insights into the distribution of activation mechanisms in this family of proteins.

PubMed: 18955063
DOI: 10.1016/j.jmb.2008.10.024

Experimental method

X-RAY DIFFRACTION (2.252 Å)