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PDBsum entry 1lm1

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protein ligands links
Oxidoreductase PDB id
1lm1
Jmol
Contents
Protein chain
1475 a.a. *
Ligands
ACT ×2
FMN
F3S
Waters ×38
* Residue conservation analysis
PDB id:
1lm1
Name: Oxidoreductase
Title: Structural studies on the synchronization of catalytic cente glutamate synthase: native enzyme
Structure: Ferredoxin-dependent glutamate synthase. Chain: a. Engineered: yes
Source: Synechocystis sp. Pcc 6803. Organism_taxid: 1148. Strain: pcc6803. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.80Å     R-factor:   0.238     R-free:   0.287
Authors: R.H.Van Den Heuvel,D.Ferrari,R.T.Bossi,S.Ravasio,B.Curti,M.A F.J.Florencio,A.Mattevi
Key ref:
R.H.van den Heuvel et al. (2002). Structural studies on the synchronization of catalytic centers in glutamate synthase. J Biol Chem, 277, 24579-24583. PubMed id: 11967268 DOI: 10.1074/jbc.M202541200
Date:
30-Apr-02     Release date:   31-Jul-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P55038  (GLTS_SYNY3) -  Ferredoxin-dependent glutamate synthase 2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1556 a.a.
1475 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.4.7.1  - Glutamate synthase (ferredoxin).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 L-glutamate + 2 oxidized ferredoxin = L-glutamine + 2-oxoglutarate + 2 reduced ferredoxin + 2 H+
2 × L-glutamate
Bound ligand (Het Group name = ACT)
matches with 40.00% similarity
+ 2 × oxidized ferredoxin
= L-glutamine
+ 2-oxoglutarate
+ 2 × reduced ferredoxin
+ 2 × H(+)
      Cofactor: FAD; FMN; Iron-sulfur
FAD
FMN
Iron-sulfur
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   7 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M202541200 J Biol Chem 277:24579-24583 (2002)
PubMed id: 11967268  
 
 
Structural studies on the synchronization of catalytic centers in glutamate synthase.
R.H.van den Heuvel, D.Ferrari, R.T.Bossi, S.Ravasio, B.Curti, M.A.Vanoni, F.J.Florencio, A.Mattevi.
 
  ABSTRACT  
 
The complex iron-sulfur flavoprotein glutamate synthase (GltS) plays a prominent role in ammonia assimilation in bacteria, yeasts, and plants. GltS catalyzes the formation of two molecules of l-glutamate from 2-oxoglutarate and l-glutamine via intramolecular channeling of ammonia. GltS has the impressive ability of synchronizing its distinct catalytic centers to avoid wasteful consumption of l-glutamine. We have determined the crystal structure of the ferredoxin-dependent GltS in several ligation and redox states. The structures reveal the crucial elements in the synchronization between the glutaminase site and the 2-iminoglutarate reduction site. The structural data combined with the catalytic properties of GltS indicate that binding of ferredoxin and 2-oxoglutarate to the FMN-binding domain of GltS induce a conformational change in the loop connecting the two catalytic centers. The rearrangement induces a shift in the catalytic elements of the amidotransferase domain, such that it becomes activated. This machinery, over a distance of more than 30 A, controls the ability of the enzyme to bind and hydrolyze the ammonia-donating substrate l-glutamine.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The overall structure of Fd-GltS with the N-terminal amidotransferase domain depicted in cornflower blue, the FMN-binding domain in yellow, the central domain in magenta, and the C-terminal domain in green. The FMN cofactor and the 3Fe-4S cluster are shown in black ball-and-stick, and the ammonia channel is outlined by red spheres. Dashed lines connect the borders of disordered loops.
Figure 3.
Fig. 3. Interdomain communication in Fd-GltS. The transparent coloring of the Fd-GltS monomer is identical to the coloring in Fig. 1 as is the orientation. Highlighted are the proposed elements involved in interdomain channeling and synchronization; Fd loop (residues 907-933), loop 4 (residues 968-1013), and loop 31-39. The FMN cofactor, 3Fe-4S cluster, and residues Cys-1 and Glu-1013 are shown as black ball-and-stick. The ammonia channel is outlined by red spheres.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 24579-24583) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20630732 H.B.Dincturk, R.Cunin, and H.Akce (2011).
Expression and functional analysis of glutamate synthase small subunit-like proteins from archaeon Pyrococcus horikoshii.
  Microbiol Res, 166, 294-303.  
20187643 L.Lund, Y.Fan, Q.Shao, Y.Q.Gao, and F.M.Raushel (2010).
Carbamate transport in carbamoyl phosphate synthetase: a theoretical and experimental investigation.
  J Am Chem Soc, 132, 3870-3878.  
19320747 J.B.Glass, F.Wolfe-Simon, and A.D.Anbar (2009).
Coevolution of metal availability and nitrogen assimilation in cyanobacteria and algae.
  Geobiology, 7, 100-123.  
19569682 Y.Fan, L.Lund, Q.Shao, Y.Q.Gao, and F.M.Raushel (2009).
A combined theoretical and experimental study of the ammonia tunnel in carbamoyl phosphate synthetase.
  J Am Chem Soc, 131, 10211-10219.  
18421771 M.A.Vanoni, and B.Curti (2008).
Structure-function studies of glutamate synthases: a class of self-regulated iron-sulfur flavoenzymes essential for nitrogen assimilation.
  IUBMB Life, 60, 287-300.  
17237175 M.Kameya, T.Ikeda, M.Nakamura, H.Arai, M.Ishii, and Y.Igarashi (2007).
A novel ferredoxin-dependent glutamate synthase from the hydrogen-oxidizing chemoautotrophic bacterium Hydrogenobacter thermophilus TK-6.
  J Bacteriol, 189, 2805-2812.  
17951049 S.Mouilleron, and B.Golinelli-Pimpaneau (2007).
Conformational changes in ammonia-channeling glutamine amidotransferases.
  Curr Opin Struct Biol, 17, 653-664.  
  17077485 A.Cámara-Artigas, M.Hirasawa, D.B.Knaff, M.Wang, and J.P.Allen (2006).
Crystallization and structural analysis of GADPH from Spinacia oleracea in a new form.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1087-1092.
PDB code: 2hki
17012385 M.Miethke, H.Westers, E.J.Blom, O.P.Kuipers, and M.A.Marahiel (2006).
Iron starvation triggers the stringent response and induces amino acid biosynthesis for bacillibactin production in Bacillus subtilis.
  J Bacteriol, 188, 8655-8657.  
16756505 N.G.Richards, and M.S.Kilberg (2006).
Asparagine synthetase chemotherapy.
  Annu Rev Biochem, 75, 629-654.  
16636918 V.Demir, and H.B.Dincturk (2006).
Semi-anaerobic growth conditions are favoured by some Escherichia coli strains during heterologous expression of some archaeal proteins.
  Mol Biol Rep, 33, 59-63.  
16143852 A.Suzuki, and D.B.Knaff (2005).
Glutamate synthase: structural, mechanistic and regulatory properties, and role in the amino acid metabolism.
  Photosynth Res, 83, 191-217.  
16143853 M.A.Vanoni, L.Dossena, R.H.van den Heuvel, and B.Curti (2005).
Structure-function studies on the complex iron-sulfur flavoprotein glutamate synthase: the key enzyme of ammonia assimilation.
  Photosynth Res, 83, 219-238.  
16143848 M.I.Muro-Pastor, J.C.Reyes, and F.J.Florencio (2005).
Ammonium assimilation in cyanobacteria.
  Photosynth Res, 83, 135-150.  
15264235 A.J.Heck, and R.H.Van Den Heuvel (2004).
Investigation of intact protein complexes by mass spectrometry.
  Mass Spectrom Rev, 23, 368-389.  
15498940 V.M.Coiro, A.Di Nola, M.A.Vanoni, M.Aschi, A.Coda, B.Curti, and D.Roccatano (2004).
Molecular dynamics simulation of the interaction between the complex iron-sulfur flavoprotein glutamate synthase and its substrates.
  Protein Sci, 13, 2979-2991.  
14622288 M.H.Hefti, J.Vervoort, and W.J.van Berkel (2003).
Deflavination and reconstitution of flavoproteins.
  Eur J Biochem, 270, 4227-4242.  
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.