2GLS

REFINED ATOMIC MODEL OF GLUTAMINE SYNTHETASE AT 3.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Refined atomic model of glutamine synthetase at 3.5 A resolution.

Yamashita, M.M.Almassy, R.J.Janson, C.A.Cascio, D.Eisenberg, D.

(1989) J Biol Chem 264: 17681-17690

  • DOI: 10.2210/pdb2gls/pdb
  • Primary Citation of Related Structures:  
    2GLS

  • PubMed Abstract: 
  • An atomic model of 43,692 non-hydrogen atoms has been determined for the 12-subunit enzyme glutamine synthetase from Salmonella typhimurium, by methods of x-ray diffraction including restrained least-squares atomic refinement against 65,223 unique reflections ...

    An atomic model of 43,692 non-hydrogen atoms has been determined for the 12-subunit enzyme glutamine synthetase from Salmonella typhimurium, by methods of x-ray diffraction including restrained least-squares atomic refinement against 65,223 unique reflections. At 3.5 A resolution the crystallographic R-factor (on 2 sigma data) is 25.8%. As reported earlier for the unrefined structure, the 12 subunits are arranged in two layers of six; at the interface of pairs of subunits within each layer, cylindrical active sites are formed by six anti-parallel beta strands contributed by one subunit and two strands by the neighboring subunit. This interpretation of the electron density map has now been supported by comparison with glutamine synthetase from Escherichia coli by the Fourier difference method. Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are Glu-131, Glu-212, and Glu-220; those to Mn2+ 470 are Glu-129, His-269, and Glu-357. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."


    Related Citations: 
    • Novel Subunit-Subunit Interactions in the Structure of Glutamine Synthetase
      Almassy, R.J., Janson, C.A., Hamlin, R., Xuong, N.-H., Eisenberg, D.
      (1986) Nature 323: 304
    • Sequence of Glutamine Synthetase from Salmonella Typhimurium and Implications for the Protein Structure
      Janson, C.A., Kayne, P.S., Almassy, R.J., Grunstein, M., Eisenberg, D.
      (1986) Gene 46: 297

    Organizational Affiliation

    Molecular Biology Institute, University of California, Los Angeles 90024.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUTAMINE SYNTHETASE
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
469Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
EC: 6.3.1.2
Find proteins for P0A1P6 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P0A1P6 
Go to UniProtKB:  P0A1P6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth H] , BA [auth H] , CA [auth I] , DA [auth I] , EA [auth J] , FA [auth J] , GA [auth K] , HA [auth K] , 
AA [auth H],  BA [auth H],  CA [auth I],  DA [auth I],  EA [auth J],  FA [auth J],  GA [auth K],  HA [auth K],  IA [auth L],  JA [auth L],  M [auth A],  N [auth A],  O [auth B],  P [auth B],  Q [auth C],  R [auth C],  S [auth D],  T [auth D],  U [auth E],  V [auth E],  W [auth F],  X [auth F],  Y [auth G],  Z [auth G]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Observed: 0.258 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 235.5α = 90
b = 134.5β = 102.8
c = 200.1γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1989-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance