Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 101.62 kDa 
• Atom Count: 6777 
• Modelled Residue Count: 870 
• Deposited Residue Count: 908 
• Unique protein chains: 1

5M7N

Crystal structure of NtrX from Brucella abortus in complex with ATP processed with the CrystalDirect automated mounting and cryo-cooling technology

• PDB DOI: 10.2210/pdb5M7N/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Brucella abortus str. 2308 A
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-28 Released: 2017-01-25 
• Deposition Author(s): Cornaciu, I., Fernandez, I., Hoffmann, G., Carrica, M.C., Goldbaum, F.A., Marquez, J.A.
• Funding Organization(s): Agencia Nacional de Promocion Cientifica y Tecnologica, BioStruct-X, iNEXT

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.238 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Three-Dimensional Structure of Full-Length NtrX, an Unusual Member of the NtrC Family of Response Regulators.

Fernandez, I., Cornaciu, I., Carrica, M.D., Uchikawa, E., Hoffmann, G., Sieira, R., Marquez, J.A., Goldbaum, F.A.

(2017) J Mol Biol 429: 1192-1212

• PubMed: 28088479 
• DOI: 10.1016/j.jmb.2016.12.022
• Primary Citation of Related Structures:  
  5M7N, 5M7O, 5M7P


• PubMed Abstract: 
  

Bacteria sense and adapt to environmental changes using two-component systems. These signaling pathways are formed by a histidine kinase that phosphorylates a response regulator (RR), which finally modulates the transcription of target genes. The bacterium Brucella abortus codes for a two-component system formed by the histidine kinase NtrY and the RR NtrX that participates in sensing low oxygen tension and generating an adaptive response. NtrX is a modular protein with REC, AAA+, and DNA-binding domains, an architecture that classifies it among the NtrC subfamily of RRs. However, it lacks the signature GAFTGA motif that is essential for activating transcription by the mechanism proposed for canonical members of this subfamily. In this article, we present the first crystal structure of full-length NtrX, which is also the first structure of a full-length NtrC-like RR with all the domains solved, showing that the protein is structurally similar to other members of the subfamily. We also report that NtrX binds nucleotides and the structures of the protein bound to ATP and ADP. Despite binding ATP, NtrX does not have ATPase activity and does not form oligomers in response to phosphorylation or nucleotide binding. We also identify a nucleotide sequence recognized by NtrX that allows it to bind to a promoter region that regulates its own transcription and to establish a negative feedback mechanism to modulate its expression. Overall, this article provides a detailed description of the NtrX RR and supports that it functions by a mechanism different to classical NtrC-like RRs.

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Organizational Affiliation: 

Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogen assimilation regulatory protein	A, B	454	Brucella abortus str. 2308 A	Mutation(s): 0  Gene Names: BAAA_2000042
UniProt
Find proteins for C4IRH0 (Brucella abortus str. 2308 A) Explore C4IRH0  Go to UniProtKB:  C4IRH0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A], F [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.238 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.867	α = 90
b = 191.611	β = 90
c = 111.702	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-10-28 
• Released Date: 2017-01-25 
Deposition Author(s): Cornaciu, I., Fernandez, I., Hoffmann, G., Carrica, M.C., Goldbaum, F.A., Marquez, J.A.

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Funding Organization	Location	Grant Number
Agencia Nacional de Promocion Cientifica y Tecnologica	Argentina	PICT-2013-1629
BioStruct-X	France	283570
iNEXT	France	653706

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-02-08
  Changes: Data collection
• Version 1.2: 2017-04-26
  Changes: Database references