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PDBsum entry 2d3b

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
2d3b
Jmol
Contents
Protein chains
(+ 4 more) 353 a.a. *
Ligands
ANP ×10
MSL ×10
Metals
_MN ×30
Waters ×377
* Residue conservation analysis
PDB id:
2d3b
Name: Ligase
Title: Crystal structure of the maize glutamine synthetase complexed with amppnp and methionine sulfoximine
Structure: Glutamine synthetase. Chain: a, b, c, d, e, f, g, h, i, j. Engineered: yes
Source: Zea mays. Organism_taxid: 4577. Gene: gs1a. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Decamer (from PQS)
Resolution:
3.50Å     R-factor:   0.168     R-free:   0.209
Authors: H.Unno,T.Uchida,H.Sugawara,G.Kurisu,T.Sugiyama,T.Yamaya, H.Sakakibara,T.Hase,M.Kusunoki
Key ref:
H.Unno et al. (2006). Atomic structure of plant glutamine synthetase: a key enzyme for plant productivity. J Biol Chem, 281, 29287-29296. PubMed id: 16829528 DOI: 10.1074/jbc.M601497200
Date:
26-Sep-05     Release date:   18-Jul-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P38561  (GLNA3_MAIZE) -  Glutamine synthetase root isozyme 3
Seq:
Struc:
356 a.a.
353 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 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
Bound ligand (Het Group name = MSL)
matches with 50.00% similarity
+ NH(3)
=
ADP
Bound ligand (Het Group name = ANP)
matches with 81.00% similarity
+ phosphate
+ L-glutamine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cell wall   5 terms 
  Biological process     nitrogen compound metabolic process   3 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M601497200 J Biol Chem 281:29287-29296 (2006)
PubMed id: 16829528  
 
 
Atomic structure of plant glutamine synthetase: a key enzyme for plant productivity.
H.Unno, T.Uchida, H.Sugawara, G.Kurisu, T.Sugiyama, T.Yamaya, H.Sakakibara, T.Hase, M.Kusunoki.
 
  ABSTRACT  
 
Plants provide nourishment for animals and other heterotrophs as the sole primary producer in the food chain. Glutamine synthetase (GS), one of the essential enzymes for plant autotrophy catalyzes the incorporation of ammonia into glutamate to generate glutamine with concomitant hydrolysis of ATP, and plays a crucial role in the assimilation and re-assimilation of ammonia derived from a wide variety of metabolic processes during plant growth and development. Elucidation of the atomic structure of higher plant GS is important to understand its detailed reaction mechanism and to obtain further insight into plant productivity and agronomical utility. Here we report the first crystal structures of maize (Zea mays L.) GS. The structure reveals a unique decameric structure that differs significantly from the bacterial GS structure. Higher plants have several isoenzymes of GS differing in heat stability and catalytic properties for efficient responses to variation in the environment and nutrition. A key residue responsible for the heat stability was found to be Ile-161 in GS1a. The three structures in complex with substrate analogues, including phosphinothricin, a widely used herbicide, lead us to propose a mechanism for the transfer of phosphate from ATP to glutamate and to interpret the inhibitory action of phosphinothricin as a guide for the development of new potential herbicides.
 
  Selected figure(s)  
 
Figure 4.
FIGURE 4. Representation of the interactions between enzyme and substrate analogues. a, stick models for the interaction of the enzyme with AMPPNP and MetSox. Carbon, oxygen, nitrogen, phosphorus, and sulfur atoms are colored gray, red, blue, salmon, and yellow, respectively. Three Mn^2+ are indicated in pink spheres. Dotted lines designate hydrogen bonds and coordination bonds to Mn^2+ ions. Residues without dotted lines have hydrophobic interactions with the substrate. b, stick models for the interaction of the enzyme with ADP and MetSox. c, stick models for the interaction of the enzyme with ADP and PPT-P.
Figure 7.
FIGURE 7. Active site structure formed by Asp-56 and Glu-297 of maize GS1a. a, stereo view of the side chain structures of Asp-56' and Glu-297 together with ADP, MetSox-P, and three Mn^2+ ions. b, alignments of short stretches of amino acid sequences containing Asp-56 and Glu-297 in GSs from M. tuberculosis (MtGS), S. typhimurium (StGS), maize (GS1 isozymes GS1a, GS1d, andGS2), Arabidopsis, human, and chicken.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 29287-29296) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21481771 J.M.van Rooyen, V.R.Abratt, H.Belrhali, and T.Sewell (2011).
Crystal Structure of Type III Glutamine Synthetase: Surprising Reversal of the Inter-Ring Interface.
  Structure, 19, 471-483.
PDB code: 3o6x
21172814 S.M.Swarbreck, M.Defoin-Platel, M.Hindle, M.Saqi, and D.Z.Habash (2011).
New perspectives on glutamine synthetase in grasses.
  J Exp Bot, 62, 1511-1522.  
20706735 B.Simon, and C.Sengupta-Gopalan (2010).
The 3' untranslated region of the two cytosolic glutamine synthetase (GS(1)) genes in alfalfa (Medicago sativa) regulates transcript stability in response to glutamine.
  Planta, 232, 1151-1162.  
20299346 C.Masclaux-Daubresse, F.Daniel-Vedele, J.Dechorgnat, F.Chardon, L.Gaufichon, and A.Suzuki (2010).
Nitrogen uptake, assimilation and remobilization in plants: challenges for sustainable and productive agriculture.
  Ann Bot, 105, 1141-1157.  
20237895 G.Estivill, P.Guardado, R.Buser, M.Betti, and A.J.Márquez (2010).
Identification of an essential cysteinyl residue for the structure of glutamine synthetase alpha from Phaseolus vulgaris.
  Planta, 231, 1101-1111.  
19448618 F.Striebel, F.Imkamp, M.Sutter, M.Steiner, A.Mamedov, and E.Weber-Ban (2009).
Bacterial ubiquitin-like modifier Pup is deamidated and conjugated to substrates by distinct but homologous enzymes.
  Nat Struct Mol Biol, 16, 647-651.  
19422547 S.M.Bernard, and D.Z.Habash (2009).
The importance of cytosolic glutamine synthetase in nitrogen assimilation and recycling.
  New Phytol, 182, 608-620.  
19097025 T.Pornprom, N.Prodmatee, and O.Chatchawankanphanich (2009).
Glutamine synthetase mutation conferring target-site-based resistance to glufosinate in soybean cell selections.
  Pest Manag Sci, 65, 216-222.  
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
18288574 S.M.Bernard, A.L.Møller, G.Dionisio, T.Kichey, T.P.Jahn, F.Dubois, M.Baudo, M.S.Lopes, T.Tercé-Laforgue, C.H.Foyer, M.A.Parry, B.G.Forde, J.L.Araus, B.Hirel, J.K.Schjoerring, and D.Z.Habash (2008).
Gene expression, cellular localisation and function of glutamine synthetase isozymes in wheat (Triticum aestivum L.).
  Plant Mol Biol, 67, 89.  
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
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.