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PDBsum entry 1ofd

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protein ligands links
Oxidoreductase PDB id
1ofd
Jmol
Contents
Protein chains
1491 a.a. *
Ligands
FMN ×2
F3S ×2
AKG ×2
Waters ×1424
* Residue conservation analysis
PDB id:
1ofd
Name: Oxidoreductase
Title: Glutamate synthase from synechocystis sp in complex with 2-oxoglutarate at 2.0 angstrom resolution
Structure: Ferredoxin-dependent glutamate synthase 2. Chain: a, b. Synonym: glutamate synthase. Engineered: yes
Source: Synechocystis sp.. Organism_taxid: 1148. Strain: pcc6803. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.194     R-free:   0.231
Authors: R.H.H.Van Den Heuvel,A.Mattevi
Key ref:
R.H.van den Heuvel et al. (2003). The active conformation of glutamate synthase and its binding to ferredoxin. J Mol Biol, 330, 113-128. PubMed id: 12818206 DOI: 10.1016/S0022-2836(03)00522-9
Date:
14-Apr-03     Release date:   11-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P55038  (GLTS_SYNY3) -  Ferredoxin-dependent glutamate synthase 2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1556 a.a.
1491 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
+ 2 × oxidized ferredoxin
= L-glutamine
+
2-oxoglutarate
Bound ligand (Het Group name = AKG)
corresponds exactly
+ 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: 10.1016/S0022-2836(03)00522-9 J Mol Biol 330:113-128 (2003)
PubMed id: 12818206  
 
 
The active conformation of glutamate synthase and its binding to ferredoxin.
R.H.van den Heuvel, D.I.Svergun, M.V.Petoukhov, A.Coda, B.Curti, S.Ravasio, M.A.Vanoni, A.Mattevi.
 
  ABSTRACT  
 
Glutamate synthases (GltS) are crucial enzymes in ammonia assimilation in plants and bacteria, where they catalyze the formation of two molecules of L-glutamate from L-glutamine and 2-oxoglutarate. The plant-type ferredoxin-dependent GltS and the functionally homologous alpha subunit of the bacterial NADPH-dependent GltS are complex four-domain monomeric enzymes of 140-165 kDa belonging to the NH(2)-terminal nucleophile family of amidotransferases. The enzymes function through the channeling of ammonia from the N-terminal amidotransferase domain to the FMN-binding domain. Here, we report the X-ray structure of the Synechocystis ferredoxin-dependent GltS with the substrate 2-oxoglutarate and the covalent inhibitor 5-oxo-L-norleucine bound in their physically distinct active sites solved using a new crystal form. The covalent Cys1-5-oxo-L-norleucine adduct mimics the glutamyl-thioester intermediate formed during L-glutamine hydrolysis. Moreover, we determined a high resolution structure of the GltS:2-oxoglutarate complex. These structures represent the enzyme in the active conformation. By comparing these structures with that of GltS alpha subunit and of related enzymes we propose a mechanism for enzyme self-regulation and ammonia channeling between the active sites. X-ray small-angle scattering experiments were performed on solutions containing GltS and its physiological electron donor ferredoxin (Fd). Using the structure of GltS and the newly determined crystal structure of Synechocystis Fd, the scattering experiments clearly showed that GltS forms an equimolar (1:1) complex with Fd. A fundamental consequence of this result is that two Fd molecules bind consecutively to Fd-GltS to yield the reduced FMN cofactor during catalysis.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Schematic representation of the reaction catalyzed by GltS. The ammonia produced in the amidotransferase domain is added onto 2-OG in the FMN-binding domain.
Figure 5.
Figure 5. (A) Presentation of the Fd-GltS active site in the FMN-binding domain with bound 2-OG and a model of bound 2-iminoglutarate. 2-OG and 2-iminoglutarate are depicted as ball-and-stick in green and red, respectively. Hydrogen bonds between Lys972 and Gln978 and the carbonyl oxygen atom of 2-OG are indicated by broken green lines. Potential hydrogen bonds between Fd-GltS and 2-iminoglutarate are indicated by broken red lines. (B) Schematic representation of the role of Lys972 and Glu903 for the dual functionality of the active site in the FMN-binding domain. Lys972 fixes 2-OG in the proper conformation for ammonia addition and polarizes the carbonyl oxygen atom. Upon ammonia addition and water release, Glu903 anchors 2-iminoglutarate in the proper conformation for reduction by FMN.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 330, 113-128) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21443874 A.Yamaoka, Y.Ozawa, Y.Ueno, T.Endo, Y.Morimoto, A.Urushiyama, D.Ohmori, and T.Imai (2011).
Cyanidioschyzon merolae ferredoxin: A high resolution crystal structure analysis and its thermal stability.
  FEBS Lett, 585, 1299-1302.  
20133651 D.Srivastava, J.P.Schuermann, T.A.White, N.Krishnan, N.Sanyal, G.L.Hura, A.Tan, M.T.Henzl, D.F.Becker, and J.J.Tanner (2010).
Crystal structure of the bifunctional proline utilization A flavoenzyme from Bradyrhizobium japonicum.
  Proc Natl Acad Sci U S A, 107, 2878-2883.
PDB code: 3haz
21070950 G.Wisedchaisri, D.M.Dranow, T.J.Lie, J.B.Bonanno, Y.Patskovsky, S.A.Ozyurt, J.M.Sauder, S.C.Almo, S.R.Wasserman, S.K.Burley, J.A.Leigh, and T.Gonen (2010).
Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR.
  Structure, 18, 1512-1521.
PDB code: 3nek
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.  
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.  
17611542 S.Dai, R.Friemann, D.A.Glauser, F.Bourquin, W.Manieri, P.Schürmann, and H.Eklund (2007).
Structural snapshots along the reaction pathway of ferredoxin-thioredoxin reductase.
  Nature, 448, 92-96.
PDB codes: 2pu9 2puk 2puo 2pvd 2pvg 2pvo
17951049 S.Mouilleron, and B.Golinelli-Pimpaneau (2007).
Conformational changes in ammonia-channeling glutamine amidotransferases.
  Curr Opin Struct Biol, 17, 653-664.  
17001090 A.Geerlof, J.Brown, B.Coutard, M.P.Egloff, F.J.Enguita, M.J.Fogg, R.J.Gilbert, M.R.Groves, A.Haouz, J.E.Nettleship, P.Nordlund, R.J.Owens, M.Ruff, S.Sainsbury, D.I.Svergun, and M.Wilmanns (2006).
The impact of protein characterization in structural proteomics.
  Acta Crystallogr D Biol Crystallogr, 62, 1125-1136.  
16339152 B.Vergauwen, D.De Vos, and J.J.Van Beeumen (2006).
Characterization of the bifunctional gamma-glutamate-cysteine ligase/glutathione synthetase (GshF) of Pasteurella multocida.
  J Biol Chem, 281, 4380-4394.  
16339762 S.Mouilleron, M.A.Badet-Denisot, and B.Golinelli-Pimpaneau (2006).
Glutamine binding opens the ammonia channel and activates glucosamine-6P synthase.
  J Biol Chem, 281, 4404-4412.
PDB codes: 2bpj 2bpl 2j6h 4amv
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.  
15593239 M.I.Catalina, R.H.van den Heuvel, E.van Duijn, and A.J.Heck (2005).
Decharging of globular proteins and protein complexes in electrospray.
  Chemistry, 11, 960-968.  
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.  
15560792 M.Sugishima, C.T.Migita, X.Zhang, T.Yoshida, and K.Fukuyama (2004).
Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC 6803 in complex with heme.
  Eur J Biochem, 271, 4517-4525.
PDB code: 1we1
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.  
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.