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PDBsum entry 1lgr

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protein ligands metals Protein-protein interface(s) links
Ligase(amide synthetase) PDB id
1lgr
Jmol
Contents
Protein chains
(+ 6 more) 445 a.a. *
Ligands
AMP ×12
Metals
_MN ×24
* Residue conservation analysis
PDB id:
1lgr
Name: Ligase(amide synthetase)
Title: Interactions of nucleotides with fully unadenylylated glutamine synthetase from salmonella typhimurium
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:
2.79Å     R-factor:   0.233    
Authors: S.-H.Liaw,D.Eisenberg
Key ref:
S.H.Liaw et al. (1994). Interactions of nucleotides with fully unadenylylated glutamine synthetase from Salmonella typhimurium. Biochemistry, 33, 11184-11188. PubMed id: 7727369 DOI: 10.1021/bi00203a014
Date:
05-Aug-94     Release date:   30-Nov-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A1P6  (GLNA_SALTY) -  Glutamine synthetase
Seq:
Struc:
469 a.a.
445 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
Bound ligand (Het Group name = AMP)
matches with 85.00% 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     cytoplasm   1 term 
  Biological process     nitrogen compound metabolic process   3 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi00203a014 Biochemistry 33:11184-11188 (1994)
PubMed id: 7727369  
 
 
Interactions of nucleotides with fully unadenylylated glutamine synthetase from Salmonella typhimurium.
S.H.Liaw, G.Jun, D.Eisenberg.
 
  ABSTRACT  
 
Glutamine synthetase (GS) catalyzes the ATP-dependent biosynthesis of glutamine from glutamate and ammonia in the presence of divalent cations. To gain insight into the structural basis of the feedback inhibition of GS by AMP, we have studied crystal structures of GS complexes with AMP and the related molecules: AMPPNP (a less hydrolyzable ATP analog), ADP, GDP, adenosine, and adenine. AMP is a feedback inhibitor of GS; ATP and ADP are cofactors, and AMPPNP, GDP, adenosine, and adenine are also GS inhibitors. GS used in this study is from Salmonella typhimurium and is free of covalent modification by adenylylation. All of the crystals examined contain two bound MN2+ ions per GS subunit. The X-ray structures show that all nucleotides bind at the same site, the cofactor ATP binding site, as do adenosine and adenine. Thus from X-ray structures, AMP, adenosine, adenine, and GDP would be expected to inhibit GS-Mn by competing with the substrate ATP for the active site. This suggestion from the crystal structures that AMP is competitive with respect to ATP is supported by kinetic measurements using the biosynthetic assay.
 

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
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
16885465 S.H.Fisher, and L.V.Wray (2006).
Feedback-resistant mutations in Bacillus subtilis glutamine synthetase are clustered in the active site.
  J Bacteriol, 188, 5966-5974.
PDB code: 2fwx
16055443 L.V.Wray, and S.H.Fisher (2005).
A feedback-resistant mutant of Bacillus subtilis glutamine synthetase with pleiotropic defects in nitrogen-regulated gene expression.
  J Biol Chem, 280, 33298-33304.  
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
12730324 L.Reitzer (2003).
Nitrogen assimilation and global regulation in Escherichia coli.
  Annu Rev Microbiol, 57, 155-176.  
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.  
10428826 J.B.Thoden, F.M.Raushel, G.Wesenberg, and H.M.Holden (1999).
The binding of inosine monophosphate to Escherichia coli carbamoyl phosphate synthetase.
  J Biol Chem, 274, 22502-22507.
PDB code: 1ce8
10024021 J.V.Lehtonen, K.Denessiouk, A.C.May, and M.S.Johnson (1999).
Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm.
  Proteins, 34, 341-355.  
  10595529 M.Eder, U.Schlattner, A.Becker, T.Wallimann, W.Kabsch, and K.Fritz-Wolf (1999).
Crystal structure of brain-type creatine kinase at 1.41 A resolution.
  Protein Sci, 8, 2258-2269.
PDB code: 1qh4
10479736 M.S.Weiss, and R.Hilgenfeld (1999).
A method to detect nonproline cis peptide bonds in proteins.
  Biopolymers, 50, 536-544.  
9434900 W.Kabsch, and K.Fritz-Wolf (1997).
Mitochondrial creatine kinase--a square protein.
  Curr Opin Struct Biol, 7, 811-818.  
  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.  
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.