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PDBsum entry 2cv2

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protein dna_rna ligands metals links
Ligase/RNA PDB id
2cv2
Jmol
Contents
Protein chains
468 a.a. *
DNA/RNA
Ligands
GSU ×2
Metals
_MG ×2
_CL ×2
Waters ×325
* Residue conservation analysis
PDB id:
2cv2
Name: Ligase/RNA
Title: Glutamyl-tRNA synthetase from thermus thermophilus in complex with tRNA(glu) and an enzyme inhibitor, glu-ams
Structure: tRNA. Chain: c, d. Engineered: yes. Glutamyl-tRNA synthetase. Chain: a, b. Synonym: glutamate--tRNA ligase, glurs. Engineered: yes
Source: Synthetic: yes. Other_details: in vitro transcription. Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.69Å     R-factor:   0.200     R-free:   0.260
Authors: S.Sekine,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
S.Sekine et al. (2006). Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase. Structure, 14, 1791-1799. PubMed id: 17161369 DOI: 10.1016/j.str.2006.10.005
Date:
31-May-05     Release date:   05-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P27000  (SYE_THET8) -  Glutamate--tRNA ligase
Seq:
Struc:
468 a.a.
468 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.17  - Glutamate--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu)
ATP
+ L-glutamate
+ tRNA(Glu)
=
AMP
Bound ligand (Het Group name = GSU)
matches with 52.00% similarity
+ diphosphate
+ L-glutamyl-tRNA(Glu)
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     translation   4 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2006.10.005 Structure 14:1791-1799 (2006)
PubMed id: 17161369  
 
 
Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase.
S.Sekine, M.Shichiri, S.Bernier, R.Chênevert, J.Lapointe, S.Yokoyama.
 
  ABSTRACT  
 
Glutamyl-tRNA synthetase (GluRS) is one of the aminoacyl-tRNA synthetases that require the cognate tRNA for specific amino acid recognition and activation. We analyzed the role of tRNA in amino acid recognition by crystallography. In the GluRS*tRNA(Glu)*Glu structure, GluRS and tRNA(Glu) collaborate to form a highly complementary L-glutamate-binding site. This collaborative site is functional, as it is formed in the same manner in pretransition-state mimic, GluRS*tRNA(Glu)*ATP*Eol (a glutamate analog), and posttransition-state mimic, GluRS*tRNA(Glu)*ESA (a glutamyl-adenylate analog) structures. In contrast, in the GluRS*Glu structure, only GluRS forms the amino acid-binding site, which is defective and accounts for the binding of incorrect amino acids, such as D-glutamate and L-glutamine. Therefore, tRNA(Glu) is essential for formation of the completely functional binding site for L-glutamate. These structures, together with our previously described structures, reveal that tRNA plays a crucial role in accurate positioning of both L-glutamate and ATP, thus driving the amino acid activation.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Glutamate Interaction Manners in the Absence and Presence of tRNA^Glu
(A) A stereo view showing the manner of glutamate recognition by the GluRS•tRNA^Glu complex in the ERS/tRNA/Glu structure. The bound glutamate, the protein amino acid residues, and A76 are colored green, white, and salmon, respectively.
(B) The GluRS-glutamate interaction in the ERS/Glu structure (stereo view). The glutamate molecule is colored yellow.
Figure 6.
Figure 6. Glutamol in ERS/tRNA/ATP/Eol and Glutamyl-Sulfamoyl Adenosine in ERS/tRNA/ESA
(A) Schematic drawings of L-glutamate (upper) and L-glutamol (Eol; lower) (Desjardins et al., 1998).
(B) Schematic drawings of L-glutamyl-adenylate (upper) and 5′-O-[N-(L-glutamyl)-sulfamoyl] adenosine (ESA; lower). ESA is a nonhydrolyzable analog of glutamyl-adenylate, and it is known as a potent competitive inhibitor of E. coli GluRS with respect to glutamic acid (K[i] = 2.8 nM) (Bernier et al., 2005).
(C) The annealed |F[o] − F[c]| omit electron density contoured at 3 σ, showing the L-glutamol molecule in ERS/tRNA/ATP/Eol. Two alternative conformations of the Eol molecule (cyan and marine) are superimposed.
(D) The omit electron density map corresponding to glutamyl-sulfamoyl adenosine in ERS/tRNA/ESA. The refined ESA model (light green) is superimposed on the density contoured at 3 σ.
 
  The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 1791-1799) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22683997 A.Palencia, T.Crépin, M.T.Vu, T.L.Lincecum, S.A.Martinis, and S.Cusack (2012).
Structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase.
  Nat Struct Mol Biol, 19, 677-684.
PDB codes: 4aq7 4arc 4ari 4as1
20606262 T.Ito, N.Kiyasu, R.Matsunaga, S.Takahashi, and S.Yokoyama (2010).
Structure of nondiscriminating glutamyl-tRNA synthetase from Thermotoga maritima.
  Acta Crystallogr D Biol Crystallogr, 66, 813-820.
PDB code: 3afh
19128026 E.M.Corigliano, and J.J.Perona (2009).
Architectural underpinnings of the genetic code for glutamine.
  Biochemistry, 48, 676-687.  
19187230 G.L.Igloi, and E.Schiefermayr (2009).
Amino acid discrimination by arginyl-tRNA synthetases as revealed by an examination of natural specificity variants.
  FEBS J, 276, 1307-1318.  
19187240 S.Paravisi, G.Fumagalli, M.Riva, P.Morandi, R.Morosi, P.V.Konarev, M.V.Petoukhov, S.Bernier, R.Chênevert, D.I.Svergun, B.Curti, and M.A.Vanoni (2009).
Kinetic and mechanistic characterization of Mycobacterium tuberculosis glutamyl-tRNA synthetase and determination of its oligomeric structure in solution.
  FEBS J, 276, 1398-1417.  
18477696 T.L.Bullock, A.Rodríguez-Hernández, E.M.Corigliano, and J.J.Perona (2008).
A rationally engineered misacylating aminoacyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 105, 7428-7433.
PDB codes: 2rd2 2re8
17726052 L.T.Guo, X.L.Chen, B.T.Zhao, Y.Shi, W.Li, H.Xue, and Y.X.Jin (2007).
Human tryptophanyl-tRNA synthetase is switched to a tRNA-dependent mode for tryptophan activation by mutations at V85 and I311.
  Nucleic Acids Res, 35, 5934-5943.  
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 codes are shown on the right.