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PDBsum entry 2gls

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protein metals Protein-protein interface(s) links
Ligase(amide synthetase) PDB id
2gls
Jmol
Contents
Protein chains
(+ 6 more) 468 a.a. *
Metals
_MN ×24
Waters ×36
* Residue conservation analysis
PDB id:
2gls
Name: Ligase(amide synthetase)
Title: Refined atomic model of glutamine synthetase at 3.5 angstrom resolution
Structure: Glutamine synthetase. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602
Biol. unit: Dodecamer (from PQS)
Resolution:
3.50Å     R-factor:   0.258    
Authors: D.Eisenberg,R.J.Almassy,M.M.Yamashita
Key ref: M.M.Yamashita et al. (1989). Refined atomic model of glutamine synthetase at 3.5 A resolution. J Biol Chem, 264, 17681-17690. PubMed id: 2572586
Date:
19-May-89     Release date:   15-Oct-89    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A1P6  (GLNA_SALTY) -  Glutamine synthetase
Seq:
Struc:
469 a.a.
468 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.6.3.1.2  - Glutamate--ammonia ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-glutamate + NH3 = ADP + phosphate + L-glutamine
ATP
+ L-glutamate
+ NH(3)
= ADP
+ phosphate
+ L-glutamine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     nitrogen compound metabolic process   3 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
J Biol Chem 264:17681-17690 (1989)
PubMed id: 2572586  
 
 
Refined atomic model of glutamine synthetase at 3.5 A resolution.
M.M.Yamashita, R.J.Almassy, C.A.Janson, D.Cascio, D.Eisenberg.
 
  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. 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."
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21256032 A.Itzen, W.Blankenfeldt, and R.S.Goody (2011).
Adenylylation: renaissance of a forgotten post-translational modification.
  Trends Biochem Sci, 36, 221-228.  
19322816 Y.X.He, L.Gui, Y.Z.Liu, Y.Du, Y.Zhou, P.Li, and C.Z.Zhou (2009).
Crystal structure of Saccharomyces cerevisiae glutamine synthetase Gln1 suggests a nanotube-like supramolecular assembly.
  Proteins, 76, 249-254.
PDB code: 3fky
17269935 E.L.Ang, J.P.Obbard, and H.Zhao (2007).
Probing the molecular determinants of aniline dioxygenase substrate specificity by saturation mutagenesis.
  FEBS J, 274, 928-939.  
17161372 K.Wyatt, H.E.White, L.Wang, O.A.Bateman, C.Slingsby, E.V.Orlova, and G.Wistow (2006).
Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens.
  Structure, 14, 1823-1834.
PDB code: 2j9i
16041744 J.Hiratake (2005).
Enzyme inhibitors as chemical tools to study enzyme catalysis: rational design, synthesis, and applications.
  Chem Rec, 5, 209-228.  
16237031 K.R.Amaya, S.A.Kocherginskaya, R.I.Mackie, and I.K.Cann (2005).
Biochemical and mutational analysis of glutamine synthetase type III from the rumen anaerobe Ruminococcus albus 8.
  J Bacteriol, 187, 7481-7491.  
15766539 S.Dutta, and H.M.Berman (2005).
Large macromolecular complexes in the Protein Data Bank: a status report.
  Structure, 13, 381-388.  
16027359 W.W.Krajewski, T.A.Jones, and S.L.Mowbray (2005).
Structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition-state mimic provides functional insights.
  Proc Natl Acad Sci U S A, 102, 10499-10504.
PDB code: 2bvc
15211520 C.Lehmann, V.Doseeva, S.Pullalarevu, W.Krajewski, A.Howard, and O.Herzberg (2004).
YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays.
  Proteins, 56, 376-383.
PDB code: 1r8g
12824490 M.I.Muro-Pastor, F.N.Barrera, J.C.Reyes, F.J.Florencio, and J.L.Neira (2003).
The inactivating factor of glutamine synthetase, IF7, is a "natively unfolded" protein.
  Protein Sci, 12, 1443-1454.  
12146952 H.S.Gill, G.M.Pfluegl, and D.Eisenberg (2002).
Multicopy crystallographic refinement of a relaxed glutamine synthetase from Mycobacterium tuberculosis highlights flexible loops in the enzymatic mechanism and its regulation.
  Biochemistry, 41, 9863-9872.
PDB codes: 1hto 1htq
12139611 S.H.Fisher, J.L.Brandenburg, and L.V.Wray (2002).
Mutations in Bacillus subtilis glutamine synthetase that block its interaction with transcription factor TnrA.
  Mol Microbiol, 45, 627-635.  
11329256 H.S.Gill, and D.Eisenberg (2001).
The crystal structure of phosphinothricin in the active site of glutamine synthetase illuminates the mechanism of enzymatic inhibition.
  Biochemistry, 40, 1903-1912.
PDB codes: 1f1h 1f52 1fpy
11238986 T.Arcondéguy, R.Jack, and M.Merrick (2001).
P(II) signal transduction proteins, pivotal players in microbial nitrogen control.
  Microbiol Mol Biol Rev, 65, 80.  
10583418 J.L.Crespo, M.G.Guerrero, and F.J.Florencio (1999).
Mutational analysis of Asp51 of Anabaena azollae glutamine synthetase. D51E mutation confers resistance to the active site inhibitors L-methionine-DL-sulfoximine and phosphinothricin.
  Eur J Biochem, 266, 1202-1209.  
10377385 M.García-Domínguez, J.C.Reyes, and F.J.Florencio (1999).
Glutamine synthetase inactivation by protein-protein interaction.
  Proc Natl Acad Sci U S A, 96, 7161-7166.  
10491091 M.T.Clemente, and A.J.Márquez (1999).
Functional importance of Asp56 from the alpha-polypeptide of Phaseolus vulgaris glutamine synthetase. An essential residue for transferase but not for biosynthetic enzyme activity.
  Eur J Biochem, 264, 453-460.  
10360178 S.E.Tsutakawa, T.Muto, T.Kawate, H.Jingami, N.Kunishima, M.Ariyoshi, D.Kohda, M.Nakagawa, and K.Morikawa (1999).
Crystallographic and functional studies of very short patch repair endonuclease.
  Mol Cell, 3, 621-628.
PDB code: 1vsr
9218784 J.A.Bertrand, G.Auger, E.Fanchon, L.Martin, D.Blanot, J.van Heijenoort, and O.Dideberg (1997).
Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli.
  EMBO J, 16, 3416-3425.
PDB codes: 1e0d 1uag
9063472 M.García-Domínguez, J.C.Reyes, and F.J.Florencio (1997).
Purification and characterization of a new type of glutamine synthetase from cyanobacteria.
  Eur J Biochem, 244, 258-264.  
  9416610 N.J.Nosworthy, and A.Ginsburg (1997).
Thermal unfolding of dodecameric glutamine synthetase: inhibition of aggregation by urea.
  Protein Sci, 6, 2617-2623.  
  8976562 L.P.Reynaldo, J.J.Villafranca, and W.D.Horrocks (1996).
Investigating the effects of posttranslational adenylylation on the metal binding sites of Escherichia coli glutamine synthetase using lanthanide luminescence spectroscopy.
  Protein Sci, 5, 2532-2544.  
7862655 C.Fan, P.C.Moews, Y.Shi, C.T.Walsh, and J.R.Knox (1995).
A common fold for peptide synthetases cleaving ATP to ADP: glutathione synthetase and D-alanine:d-alanine ligase of Escherichia coli.
  Proc Natl Acad Sci U S A, 92, 1172-1176.  
  7603411 K.E.Sanderson, A.Hessel, and K.E.Rudd (1995).
Genetic map of Salmonella typhimurium, edition VIII.
  Microbiol Rev, 59, 241-303.  
  8531888 M.J.Merrick, and R.A.Edwards (1995).
Nitrogen control in bacteria.
  Microbiol Rev, 59, 604-622.  
  8520480 M.Zolkiewski, N.J.Nosworthy, and A.Ginsburg (1995).
Urea-induced dissociation and unfolding of dodecameric glutamine synthetase from Escherichia coli: calorimetric and spectral studies.
  Protein Sci, 4, 1544-1552.  
  8563633 S.H.Liaw, I.Kuo, and D.Eisenberg (1995).
Discovery of the ammonium substrate site on glutamine synthetase, a third cation binding site.
  Protein Sci, 4, 2358-2365.  
  7912599 A.M.Dhalla, B.Li, M.F.Alibhai, K.J.Yost, J.M.Hemmingsen, W.M.Atkins, J.Schineller, and J.J.Villafranca (1994).
Regeneration of catalytic activity of glutamine synthetase mutants by chemical activation: exploration of the role of arginines 339 and 359 in activity.
  Protein Sci, 3, 476-481.  
8052629 G.L.Eichhorn, P.P.Chuknyisky, J.J.Butzow, R.B.Beal, C.Garland, C.P.Janzen, P.Clark, and E.Tarien (1994).
A structural model for fidelity in transcription.
  Proc Natl Acad Sci U S A, 91, 7613-7617.  
  7906687 J.C.Reyes, and F.J.Florencio (1994).
A new type of glutamine synthetase in cyanobacteria: the protein encoded by the glnN gene supports nitrogen assimilation in Synechocystis sp. strain PCC 6803.
  J Bacteriol, 176, 1260-1267.  
7981719 J.G.Vockley, D.E.Tabor, R.M.Kern, B.K.Goodman, P.B.Wissmann, D.S.Kang, W.W.Grody, and S.D.Cederbaum (1994).
Identification of mutations (D128G, H141L) in the liver arginase gene of patients with hyperargininemia.
  Hum Mutat, 4, 150-154.  
  7849593 M.R.Witmer, D.Palmieri-Young, and J.J.Villafranca (1994).
Probing the catalytic roles of n2-site glutamate residues in Escherichia coli glutamine synthetase by mutagenesis.
  Protein Sci, 3, 1746-1759.  
  8093698 H.J.Schreier, C.A.Rostkowski, and E.M.Kellner (1993).
Altered regulation of the glnRA operon in a Bacillus subtilis mutant that produces methionine sulfoximine-tolerant glutamine synthetase.
  J Bacteriol, 175, 892-897.  
8099447 S.H.Liaw, C.Pan, and D.Eisenberg (1993).
Feedback inhibition of fully unadenylylated glutamine synthetase from Salmonella typhimurium by glycine, alanine, and serine.
  Proc Natl Acad Sci U S A, 90, 4996-5000.
PDB code: 2lgs
  8095834 S.H.Liaw, G.Jun, and D.Eisenberg (1993).
Extending the diffraction limit of protein crystals: the example of glutamine synthetase from Salmonella typhimurium in the presence of its cofactor ATP.
  Protein Sci, 2, 470-471.  
1579569 A.L.Morris, M.W.MacArthur, E.G.Hutchinson, and J.M.Thornton (1992).
Stereochemical quality of protein structure coordinates.
  Proteins, 12, 345-364.  
  1363912 W.M.Atkins, and J.J.Villafranca (1992).
Time-resolved fluorescence studies of tryptophan mutants of Escherichia coli glutamine synthetase: conformational analysis of intermediates and transition-state complexes.
  Protein Sci, 1, 342-355.  
  1683868 A.Contreras, M.Drummond, A.Bali, G.Blanco, E.Garcia, G.Bush, C.Kennedy, and M.Merrick (1991).
The product of the nitrogen fixation regulatory gene nfrX of Azotobacter vinelandii is functionally and structurally homologous to the uridylyltransferase encoded by glnD in enteric bacteria.
  J Bacteriol, 173, 7741-7749.  
  2041094 D.J.Thomas, J.S.Wall, J.F.Hainfeld, M.Kaczorek, F.P.Booy, B.L.Trus, F.A.Eiserling, and A.C.Steven (1991).
gp160, the envelope glycoprotein of human immunodeficiency virus type 1, is a dimer of 125-kilodalton subunits stabilized through interactions between their gp41 domains.
  J Virol, 65, 3797-3803.  
1671172 G.Pesole, M.P.Bozzetti, C.Lanave, G.Preparata, and C.Saccone (1991).
Glutamine synthetase gene evolution: a good molecular clock.
  Proc Natl Acad Sci U S A, 88, 522-526.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.