1WDN

GLUTAMINE-BINDING PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of glutamine-binding protein complexed with glutamine at 1.94 A resolution: comparisons with other amino acid binding proteins.

Sun, Y.J.Rose, J.Wang, B.C.Hsiao, C.D.

(1998) J.Mol.Biol. 278: 219-229

  • DOI: 10.1006/jmbi.1998.1675

  • PubMed Abstract: 
  • The crystal structure of the glutamine-binding protein (GlnBP) complexed with its ligand (Gln) was determined and refined to 1.94 A resolution. This ellipsoidal protein has two globular domains and is approximately 52 Ax40 Ax35 A in size. The glutami ...

    The crystal structure of the glutamine-binding protein (GlnBP) complexed with its ligand (Gln) was determined and refined to 1.94 A resolution. This ellipsoidal protein has two globular domains and is approximately 52 Ax40 Ax35 A in size. The glutamine ligand is located in the cleft between the two domains and stablized by hydrogen bondings and ionic interactions with Asp10, Gly68, Thr70, Ala67, Asp157, Arg75, Lys115, Gly119 and His156. The aliphatic portion of the glutamine ligand is sandwiched in a hydrophobic pocket formed between Phe13 and Phe50 and has 21 van der Waals contacts with GlnBP. Lys115 and His156, that are unique to GlnBP among amino acid binding proteins, apparently contribute to the ligand binding specificity of GlnBP. Asp10 is within 3 A of Lys115. These two residues are over 10 A apart in the ligand-free form of the GlnBP. In addition, GlnBP-Gln exhibits a large-scale movement of the two hinges connecting the two globular domains upon ligand binding. The most significant changes are 41.1 degrees in the phi angle of Gly89 and 34.3 degrees in the psi angle of Glu181 from the first and the second hinge of the protein, respectively. Besides the original six hydrogen bonds, three extra hydrogen bonds can be observed between the two hinge strands upon ligand binding. A hydrogen bond network connects the large domain to the second hinge and a second hydrogen bond network coalesces the small domain to the same strand, both via interaction with the glutamine ligand. Although the two strands of the hinge connecting the domains do not directly participate in the ligand binding, Gln183 and Tyr185 from the second hinge may be involved in the cascade of the conformational change that is induced by ligand binding.


    Related Citations: 
    • The Crystal Structure of Glutamine-Binding Protein from Escherichia Coli
      Hsiao, C.D.,Sun, Y.J.,Rose, J.,Wang, B.C.
      (1996) J.Mol.Biol. 262: 225
    • Crystals of Glutamine-Binding Protein in Various Conformational States
      Hsiao, C.D.,Sun, Y.J.,Rose, J.,Cottam, P.F.,Ho, C.,Wang, B.C.
      (1994) J.Mol.Biol. 240: 87
    • Preliminary Crystallographic Analysis of Glutamine-Binding Protein from Escherichia Coli
      Chen, P.,Rose, J.,Chung, Y.J.,Wang, B.C.,Shen, Q.C.,Cottam, P.F.,Ho, C.
      (1989) J.Mol.Biol. 205: 459


    Organizational Affiliation

    Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, 11529, Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMINE BINDING PROTEIN
A
226Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: glnH
Find proteins for P0AEQ3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEQ3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLN
Query on GLN

Download SDF File 
Download CCD File 
A
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GLNKd: 500 nM BINDINGMOAD
GLNKd: 500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.700α = 90.00
b = 91.000β = 90.00
c = 34.700γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-06
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance