4Z9I

Asp-TarS from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Analysis of the Ligand-Binding Domain of the Aspartate Receptor Tar from Escherichia coli

Mise, T.

(2016) Biochemistry 55: 3708-3713

  • DOI: 10.1021/acs.biochem.6b00160
  • Primary Citation of Related Structures:  
    4Z9H, 4Z9I, 4Z9J

  • PubMed Abstract: 
  • The Escherichia coli cell-surface aspartate receptor Tar mediates bacterial chemotaxis toward an attractant, aspartate (Asp), and away from a repellent, Ni(2+). These signals are transmitted from the extracellular region of Tar to the cytoplasmic region via the transmembrane domain ...

    The Escherichia coli cell-surface aspartate receptor Tar mediates bacterial chemotaxis toward an attractant, aspartate (Asp), and away from a repellent, Ni(2+). These signals are transmitted from the extracellular region of Tar to the cytoplasmic region via the transmembrane domain. The mechanism by which extracellular signals are transmitted into the cell through conformational changes in Tar is predicted to involve a piston displacement of one of the α4 helices of the homodimer. To understand the molecular mechanisms underlying the induction of Tar activity by an attractant, the three-dimensional structures of the E. coli Tar periplasmic domain with and without bound aspartate, Asp-Tar and apo-Tar, respectively, were determined. Of the two ligand-binding sites, only one site was occupied, and it clearly showed the electron density of an aspartate. The slight changes in conformation and the electrostatic surface potential around the aspartate-binding site were observed. In addition, the presence of an aspartate stabilized residues Phe-150' and Arg-73. A pistonlike displacement of helix α4b' was also induced by aspartate binding as predicted by the piston model. Taken together, these small changes might be related to the induction of Tar activity and might disturb binding of the second aspartate to the second binding site in E. coli.


    Organizational Affiliation

    2-19-3 Misato, Okinawa-shi, Okinawa 904-2153, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methyl-accepting chemotaxis protein IIA, B196Escherichia coli K-12Mutation(s): 0 
Gene Names: tarcheMb1886JW1875
UniProt
Find proteins for P07017 (Escherichia coli (strain K12))
Explore P07017 
Go to UniProtKB:  P07017
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07017
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ASP
Query on ASP

Download Ideal Coordinates CCD File 
C [auth B]ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.46α = 90
b = 59.51β = 95.02
c = 79.38γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
iMOSFLMdata reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2015-04-10 
  • Released Date: 2016-07-20 
  • Deposition Author(s): Mise, T.

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection, Derived calculations