PDBsum entry 3dzd

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Transcription regulator PDB id
Protein chains
368 a.a. *
ADP ×2
Waters ×250
* Residue conservation analysis
PDB id:
Name: Transcription regulator
Title: Crystal structure of sigma54 activator ntrc4 in the inactive state
Structure: Transcriptional regulator (ntrc family). Chain: a, b. Fragment: unp residues 2 to 369. Engineered: yes
Source: Aquifex aeolicus. Organism_taxid: 63363. Gene: aq_164, ntrc4. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.40Å     R-factor:   0.216     R-free:   0.262
Authors: J.D.Batchelor,M.Doucleff,C.-J.Lee,K.Matsubara,S.De Carlo, J.Heideker,M.M.Lamers,J.G.Pelton,D.E.Wemmer
Key ref:
J.D.Batchelor et al. (2008). Structure and regulatory mechanism of Aquifex aeolicus NtrC4: variability and evolution in bacterial transcriptional regulation. J Mol Biol, 384, 1058-1075. PubMed id: 18955063 DOI: 10.1016/j.jmb.2008.10.024
29-Jul-08     Release date:   25-Nov-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O66551  (O66551_AQUAE) -  Transcriptional regulator (NtrC family)
442 a.a.
368 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     two-component signal transduction system (phosphorelay)   2 terms 
  Biochemical function     nucleotide binding     5 terms  


DOI no: 10.1016/j.jmb.2008.10.024 J Mol Biol 384:1058-1075 (2008)
PubMed id: 18955063  
Structure and regulatory mechanism of Aquifex aeolicus NtrC4: variability and evolution in bacterial transcriptional regulation.
J.D.Batchelor, M.Doucleff, C.J.Lee, K.Matsubara, S.De Carlo, J.Heideker, M.H.Lamers, J.G.Pelton, D.E.Wemmer.
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.
  Selected figure(s)  
Figure 6.
Fig. 6. Ribbon diagram of the crystal structure of the dimeric DNA-binding domain of NtrC4.
Figure 10.
Fig. 10. The receiver domain dimer interface for NtrC4 is shown. (a) The active dimer interface showing side chains of K93, D98, I92, V89, A88, and V85. (b) The unactivated dimer interface showing side chains of H115, R108, Y97, and D98. (c) The active receiver dimer showing side chains of Y97, H115, V89, and I92. (d) The unactivated receiver dimer showing the same side chains as (c).
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 384, 1058-1075) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20226685 H.J.Sterling, J.D.Batchelor, D.E.Wemmer, and E.R.Williams (2010).
Effects of buffer loading for electrospray ionization mass spectrometry of a noncovalent protein complex that requires high concentrations of essential salts.
  J Am Soc Mass Spectrom, 21, 1045-1049.  
20624215 M.Bush, T.Ghosh, N.Tucker, X.Zhang, and R.Dixon (2010).
Nitric oxide-responsive interdomain regulation targets the σ54-interaction surface in the enhancer binding protein NorR.
  Mol Microbiol, 77, 1278-1288.  
20226724 M.Y.Galperin (2010).
Diversity of structure and function of response regulator output domains.
  Curr Opin Microbiol, 13, 150-159.  
20080056 R.Gao, and A.M.Stock (2010).
Molecular strategies for phosphorylation-mediated regulation of response regulator activity.
  Curr Opin Microbiol, 13, 160-167.  
19682923 H.J.Sterling, and E.R.Williams (2009).
Origin of supercharging in electrospray ionization of noncovalent complexes from aqueous solution.
  J Am Soc Mass Spectrom, 20, 1933-1943.  
19699748 J.D.Batchelor, H.J.Sterling, E.Hong, E.R.Williams, and D.E.Wemmer (2009).
Receiver domains control the active-state stoichiometry of Aquifex aeolicus sigma54 activator NtrC4, as revealed by electrospray ionization mass spectrometry.
  J Mol Biol, 393, 634-643.  
19575571 R.Gao, and A.M.Stock (2009).
Biological insights from structures of two-component proteins.
  Annu Rev Microbiol, 63, 133-154.  
19246239 U.Jenal, and M.Y.Galperin (2009).
Single domain response regulators: molecular switches with emerging roles in cell organization and dynamics.
  Curr Opin Microbiol, 12, 152-160.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.