1LGR | pdb_00001lgr

INTERACTIONS OF NUCLEOTIDES WITH FULLY UNADENYLYLATED GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Work: 
    0.233 (Depositor) 
  • R-Value Observed: 
    0.233 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Interactions of nucleotides with fully unadenylylated glutamine synthetase from Salmonella typhimurium.

Liaw, S.H.Jun, G.Eisenberg, D.

(1994) Biochemistry 33: 11184-11188

  • DOI: https://doi.org/10.1021/bi00203a014
  • Primary Citation Related Structures: 
    1LGR

  • PubMed Abstract: 

    Glutamine synthetase (GS) catalyzes the ATP-dependent biosynthesis of glutamine from glutamate and ammonia in the presence of divalent cations. To gain insight into the structural basis of the feedback inhibition of GS by AMP, we have studied crystal structures of GS complexes with AMP and the related molecules: AMPPNP (a less hydrolyzable ATP analog), ADP, GDP, adenosine, and adenine. AMP is a feedback inhibitor of GS; ATP and ADP are cofactors, and AMPPNP, GDP, adenosine, and adenine are also GS inhibitors. GS used in this study is from Salmonella typhimurium and is free of covalent modification by adenylylation. All of the crystals examined contain two bound MN2+ ions per GS subunit. The X-ray structures show that all nucleotides bind at the same site, the cofactor ATP binding site, as do adenosine and adenine. Thus from X-ray structures, AMP, adenosine, adenine, and GDP would be expected to inhibit GS-Mn by competing with the substrate ATP for the active site. This suggestion from the crystal structures that AMP is competitive with respect to ATP is supported by kinetic measurements using the biosynthetic assay.


  • Organizational Affiliation
    • Institute of Molecular Medicine, School of Medicine, National Taiwan University, Taipei.

Macromolecule Content 

  • Total Structure Weight: 626.42 kDa 
  • Atom Count: 41,760 
  • Modeled Residue Count: 5,340 
  • Deposited Residue Count: 5,616 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLUTAMINE SYNTHETASE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
468Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
EC: 6.3.1.2
UniProt
Find proteins for P0A1P6 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P0A1P6 
Go to UniProtKB:  P0A1P6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A1P6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP

Query on AMP



Download:Ideal Coordinates CCD File
AA [auth E]
DA [auth F]
GA [auth G]
JA [auth H]
MA [auth I]
AA [auth E],
DA [auth F],
GA [auth G],
JA [auth H],
MA [auth I],
O [auth A],
PA [auth J],
R [auth B],
SA [auth K],
U [auth C],
VA [auth L],
X [auth D]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
BA [auth F]
CA [auth F]
EA [auth G]
FA [auth G]
HA [auth H]
BA [auth F],
CA [auth F],
EA [auth G],
FA [auth G],
HA [auth H],
IA [auth H],
KA [auth I],
LA [auth I],
M [auth A],
N [auth A],
NA [auth J],
OA [auth J],
P [auth B],
Q [auth B],
QA [auth K],
RA [auth K],
S [auth C],
T [auth C],
TA [auth L],
UA [auth L],
V [auth D],
W [auth D],
Y [auth E],
Z [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Work:  0.233 (Depositor) 
  • R-Value Observed: 0.233 (Depositor) 
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
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-11-30
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Other