Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 84.77 kDa 
• Atom Count: 6203 
• Residue Count: 736 
• Unique protein chains: 1

3DZD

Crystal structure of sigma54 activator NTRC4 in the inactive state

• DOI: 10.2210/pdb3DZD/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-29 Released: 2008-11-25 
• Deposition Author(s): Batchelor, J.D., Doucleff, M., Lee, C.-J., Matsubara, K., De Carlo, S., Heideker, J., Lamers, M.M., Pelton, J.G., Wemmer, D.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.262 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

Structure and regulatory mechanism of Aquifex aeolicus NtrC4: variability and evolution in bacterial transcriptional regulation.

Batchelor, J.D., Doucleff, M., Lee, C.J., Matsubara, K., De Carlo, S., Heideker, J., Lamers, M.H., Pelton, J.G., Wemmer, D.E.

(2008) J Mol Biol 384: 1058-1075

• PubMed: 18955063 
• DOI: 10.1016/j.jmb.2008.10.024
• Primary Citation of Related Structures:  
  3E7L, 3DZD


• 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.

---

Organizational Affiliation: 

Graduate Group in Biophysics, Physical Biosciences Division, Lawrence Berkeley National Laboratory and the Department of Chemistry, University of California, Berkeley, CA 94720, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator (NtrC family)	A, B	368	Aquifex aeolicus	Mutation(s): 0  Gene Names: aq_164, ntrC4
Find proteins for O66551 (Aquifex aeolicus (strain VF5)) Explore O66551  Go to UniProtKB:  O66551

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	A, B	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
NA	B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.262 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.897	α = 90
b = 93.105	β = 90
c = 114.163	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
RESOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-07-29 
• Released Date: 2008-11-25 
Deposition Author(s): Batchelor, J.D., Doucleff, M., Lee, C.-J., Matsubara, K., De Carlo, S., Heideker, J., Lamers, M.M., Pelton, J.G., Wemmer, D.E.

Revision History 

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance