2PYY

Crystal Structure of the GluR0 ligand-binding core from Nostoc punctiforme in complex with (L)-glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the GluR0 ligand-binding core from Nostoc punctiforme in complex with L-glutamate: structural dissection of the ligand interaction and subunit interface.

Lee, J.H.Kang, G.B.Lim, H.H.Jin, K.S.Kim, S.H.Ree, M.Park, C.S.Kim, S.J.Eom, S.H.

(2008) J.Mol.Biol. 376: 308-316

  • DOI: 10.1016/j.jmb.2007.10.081

  • PubMed Abstract: 
  • GluR0 from Nostoc punctiforme (NpGluR0) is a bacterial homologue of the ionotropic glutamate receptor (iGluR). We have solved the crystal structure of the ligand-binding core of NpGluR0 in complex with l-glutamate at a resolution of 2.1 A. The struct ...

    GluR0 from Nostoc punctiforme (NpGluR0) is a bacterial homologue of the ionotropic glutamate receptor (iGluR). We have solved the crystal structure of the ligand-binding core of NpGluR0 in complex with l-glutamate at a resolution of 2.1 A. The structure exhibits a noncanonical ligand interaction and two distinct subunit interfaces. The side-chain guanidium group of Arg80 forms a salt bridge with the gamma-carboxyl group of bound L-glutamate: in GluR0 from Synechocystis (SGluR0) and other iGluRs, the equivalent residues are Asn or Thr, which cannot form a similar interaction. We suggest that the local positively charged environment and the steric constraint created by Arg80 mediate the selectivity of L-glutamate binding by preventing the binding of positively charged and hydrophobic amino acids. In addition, the NpGluR0 ligand-binding core forms a new subunit interface in which the two protomers are arranged differently than the known iGluR and SGluR0 dimer interfaces. The significance of there being two different dimer interfaces was investigated using analytical ultracentrifugation analysis.


    Organizational Affiliation

    Department of Life Science, Cell Dynamics Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju 500-712, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ionotropic glutamate receptor bacterial homologue
A, B, C
228Nostoc punctiforme (strain ATCC 29133 / PCC 73102)Mutation(s): 0 
Find proteins for D0VWX9 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102))
Go to UniProtKB:  D0VWX9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

Download SDF File 
Download CCD File 
A, B, C
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GLUKd: 200 nM BINDINGMOAD
GLUKd: 25000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.233 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 77.979α = 90.00
b = 145.085β = 90.00
c = 132.128γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
MOLREPphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance