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3DZD

Crystal structure of sigma54 activator NTRC4 in the inactive state

Summary for 3DZD
Entry DOI10.2210/pdb3dzd/pdb
Related3E7L
DescriptorTranscriptional regulator (NtrC family), ADENOSINE-5'-DIPHOSPHATE, SODIUM ION, ... (4 entities in total)
Functional Keywordssigma43 activator, aaa+ atpase, response regulator, transcriptional activator, atp-binding, nucleotide-binding, transcription, transcription regulation, transcription regulator
Biological sourceAquifex aeolicus
Total number of polymer chains2
Total formula weight84773.42
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: 2008-07-29, release date: 2008-11-25, Last modification date: 2024-11-13)
Primary citationBatchelor, 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
Cited by
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
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.4 Å)
Structure validation

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