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PDBsum entry 3fky

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protein ligands Protein-protein interface(s) links
Ligase PDB id
3fky
Jmol
Contents
Protein chains
(+ 14 more) 336 a.a. *
Ligands
FLC ×20
* Residue conservation analysis
PDB id:
3fky
Name: Ligase
Title: Crystal structure of the glutamine synthetase gln1deltan18 from the yeast saccharomyces cerevisiae
Structure: Glutamine synthetase. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t. Synonym: gs, glutamate--ammonia ligase. Engineered: yes
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Strain: s288c. Gene: gln1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.95Å     R-factor:   0.226     R-free:   0.258
Authors: Y.X.He,L.Gui,Y.Z.Liu,Y.Du,Y.Y.Zhou,P.Li,C.Z.Zhou
Key ref:
Y.X.He et al. (2009). Crystal structure of Saccharomyces cerevisiae glutamine synthetase Gln1 suggests a nanotube-like supramolecular assembly. Proteins, 76, 249-254. PubMed id: 19322816 DOI: 10.1002/prot.22403
Date:
18-Dec-08     Release date:   06-Oct-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P32288  (GLNA_YEAST) -  Glutamine synthetase
Seq:
Struc:
370 a.a.
336 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 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 = FLC)
matches with 64.00% similarity
+ 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   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1002/prot.22403 Proteins 76:249-254 (2009)
PubMed id: 19322816  
 
 
Crystal structure of Saccharomyces cerevisiae glutamine synthetase Gln1 suggests a nanotube-like supramolecular assembly.
Y.X.He, L.Gui, Y.Z.Liu, Y.Du, Y.Zhou, P.Li, C.Z.Zhou.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. (A) Multialignment of GSII enzymes. The alignment was performed using MultAlin and ESPript.[25][26] The secondary structural elements are identified from the structure of Gln1 and displayed at the top of the alignment. The -helices, -helices, -sheets, and strict -turns are denoted as , , , and TT, correspondingly. The residues involved in citrate binding were marked by black stars. (B) Cartoon representation of the Gln1 monomer. The N-terminal -grasp domain was colored in purple and the C-terminal catalytic domain was colored in green. The bound citrate ion was shown in sticks. (C) Superposition of Gln1 (blue) and human GSII in complex with Mn^2+, ADP, and the inhibitor MSO-P (red). The regions undergoing large conformational changes were indicated with black arrows. Two neighboring subunits in the pentameric ring were used for the superposition. Only the catalytic domain from one subunit and the neighboring -grasp domain from the other were shown in cartoon representation. The citrate was shown in pink sticks, ADP and MSO-P in golden sticks, and manganese in gray spheres.
Figure 2.
Figure 2. Oligomeric structure of Gln1. (A) Cartoon representation of four stacking pentameric rings in one asymmetry unit, designated as pentamer I, II, III, and IV. (B) Gln1 decamer composed of pentamer I and pentamer II at the top view. (C) The novel back-to-back pentameric ring association involving pentamer II and pentamer III at the top view. For B and C, the pentagons were drawn using the active sites (positions of His250) as vertices in each pentamer.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2009, 76, 249-254) copyright 2009.  

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
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.  
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.