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PDBsum entry 1n75

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protein ligands metals links
Ligase PDB id
1n75
Jmol
Contents
Protein chain
468 a.a. *
Ligands
ATP
Metals
_MG
Waters ×347
* Residue conservation analysis
PDB id:
1n75
Name: Ligase
Title: Crystal structure of thermus thermophilus glutamyl-tRNA synthetase complexed with atp.
Structure: Glutamyl-tRNA synthetase. Chain: a. Synonym: glurs, glutamate--tRNA ligase. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.90Å     R-factor:   0.209     R-free:   0.236
Authors: S.Sekine,O.Nureki,D.Y.Dubois,S.Bernier,R.Chenevert, J.Lapointe,D.G.Vassylyev,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
S.Sekine et al. (2003). ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. EMBO J, 22, 676-688. PubMed id: 12554668 DOI: 10.1093/emboj/cdg053
Date:
12-Nov-02     Release date:   25-Feb-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
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
Bound ligand (Het Group name = ATP)
corresponds exactly
+ L-glutamate
+ tRNA(Glu)
= AMP
+ 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: 10.1093/emboj/cdg053 EMBO J 22:676-688 (2003)
PubMed id: 12554668  
 
 
ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding.
S.Sekine, O.Nureki, D.Y.Dubois, S.Bernier, R.Chênevert, J.Lapointe, D.G.Vassylyev, S.Yokoyama.
 
  ABSTRACT  
 
Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl-tRNA synthetases, including glutamyl-tRNA synthetase (GluRS), have a regulation mechanism to avoid aminoacyl-AMP formation in the absence of tRNA. In this study, we determined the crystal structure of the 'non-productive' complex of Thermus thermophilus GluRS, ATP and L-glutamate, together with those of the GluRS.ATP, GluRS.tRNA.ATP and GluRS.tRNA.GoA (a glutamyl-AMP analog) complexes. In the absence of tRNA(Glu), ATP is accommodated in a 'non-productive' subsite within the ATP-binding site, so that the ATP alpha-phosphate and the glutamate alpha-carboxyl groups in GluRS. ATP.Glu are too far from each other (6.2 A) to react. In contrast, the ATP-binding mode in GluRS.tRNA. ATP is dramatically different from those in GluRS.ATP.Glu and GluRS.ATP, but corresponds to the AMP moiety binding mode in GluRS.tRNA.GoA (the 'productive' subsite). Therefore, tRNA binding to GluRS switches the ATP-binding mode. The interactions of the three tRNA(Glu) regions with GluRS cause conformational changes around the ATP-binding site, and allow ATP to bind to the 'productive' subsite.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Thermus thermophilus GluRS crystal structures. (A) Ribbon representation of the ERS/ATP/Glu structure. Five domains, the Rossmann fold (1), connective peptide (or acceptor-binding) (2), stem-contact fold (3) and two anticodon-binding (4 and 5) domains, are colored khaki, light blue, pink, steel blue and deep blue, respectively. The HVGT and KISKR motifs of GluRS are highlighted in purple. The ATP and glutamate molecules in the GluRS catalytic pocket are shown in green. (B) Overall structure of ERS/tRNA/ATP. The ATP and tRNA^Glu molecules in the complex are shown in orange and turquoise, respectively. These figures were produced using the MOLSCRIPT (Kraulis, 1991) and RASTER3D (Merritt and Murphy, 1994) programs.
Figure 4.
Figure 4 Substrate/ligand(s) binding in the GluRS complexes. (A -D) The GluRS catalytic site structures in the present complexes are shown in the same orientation. The HVGT and KISKR motifs are highlighted in purple. (A) The ERS/ATP/Glu structure. The ATP-Mg2+ and glutamate molecules are shown in green. (B) The ERS/ATP structure. The ATP-Mg2+ is colored light blue. (C) The ERS/tRNA/ATP structure. The ATP molecule is colored salmon, and the 3'-terminal adenosine (A76) of tRNA^Glu is cyan. (D) The ERS/tRNA/GoA structure. The GoA (glutamol-AMP) molecule is colored yellow. (E) A stereo view showing the ATP recognition in ERS/tRNA/ATP. (F) A stereo view showing the GoA recognition in ERS/tRNA/GoA.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2003, 22, 676-688) copyright 2003.  
  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
20541532 A.Katz, R.Banerjee, M.de Armas, M.Ibba, and O.Orellana (2010).
Redox status affects the catalytic activity of glutamyl-tRNA synthetase.
  Biochem Biophys Res Commun, 398, 51-55.  
21127037 G.Kawai, and S.Yokoyama (2010).
Professor Tatsuo Miyazawa: from molecular structure to biological function.
  J Biochem, 148, 631-638.  
20882017 T.Ito, and S.Yokoyama (2010).
Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions.
  Nature, 467, 612-616.
PDB codes: 3akz 3al0
20057044 V.B.Chen, W.B.Arendall, J.J.Headd, D.A.Keedy, R.M.Immormino, G.J.Kapral, L.W.Murray, J.S.Richardson, and D.C.Richardson (2010).
MolProbity: all-atom structure validation for macromolecular crystallography.
  Acta Crystallogr D Biol Crystallogr, 66, 12-21.  
  19610673 A.M.Gulick (2009).
Conformational dynamics in the Acyl-CoA synthetases, adenylation domains of non-ribosomal peptide synthetases, and firefly luciferase.
  ACS Chem Biol, 4, 811-827.  
19351898 A.Sethi, J.Eargle, A.A.Black, and Z.Luthey-Schulten (2009).
Dynamical networks in tRNA:protein complexes.
  Proc Natl Acad Sci U S A, 106, 6620-6625.  
19656186 M.Konno, T.Sumida, E.Uchikawa, Y.Mori, T.Yanagisawa, S.Sekine, and S.Yokoyama (2009).
Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP).
  FEBS J, 276, 4763-4779.
PDB codes: 2zue 2zuf
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.  
18850722 C.S.Francklyn (2008).
DNA polymerases and aminoacyl-tRNA synthetases: shared mechanisms for ensuring the fidelity of gene expression.
  Biochemistry, 47, 11695-11703.  
17910059 J.J.Ellis, and S.Jones (2008).
Evaluating conformational changes in protein structures binding RNA.
  Proteins, 70, 1518-1526.  
18276647 Y.C.Chen, and C.Lim (2008).
Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry.
  Nucleic Acids Res, 36, e29.  
17447878 I.A.Vasil'eva, and N.A.Moor (2007).
Interaction of aminoacyl-tRNA synthetases with tRNA: general principles and distinguishing characteristics of the high-molecular-weight substrate recognition.
  Biochemistry (Mosc), 72, 247-263.  
17510965 M.E.Budiman, M.H.Knaggs, J.S.Fetrow, and R.W.Alexander (2007).
Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase.
  Proteins, 68, 670-689.  
17937916 M.Kapustina, V.Weinreb, L.Li, B.Kuhlman, and C.W.Carter (2007).
A conformational transition state accompanies tryptophan activation by B. stearothermophilus tryptophanyl-tRNA synthetase.
  Structure, 15, 1272-1284.  
17428498 P.Retailleau, V.Weinreb, M.Hu, and C.W.Carter (2007).
Crystal structure of tryptophanyl-tRNA synthetase complexed with adenosine-5' tetraphosphate: evidence for distributed use of catalytic binding energy in amino acid activation by class I aminoacyl-tRNA synthetases.
  J Mol Biol, 369, 108-128.
PDB code: 2ov4
17507661 R.Tyagi, and D.H.Mathews (2007).
Predicting helical coaxial stacking in RNA multibranch loops.
  RNA, 13, 939-951.  
17532006 Y.Devedjiev, C.N.Steussy, and D.G.Vassylyev (2007).
Crystal structure of an asymmetric complex of pyruvate dehydrogenase kinase 3 with lipoyl domain 2 and its biological implications.
  J Mol Biol, 370, 407-416.
PDB code: 2pnr
16533047 S.Wang, M.Praetorius-Ibba, S.F.Ataide, H.Roy, and M.Ibba (2006).
Discrimination of cognate and noncognate substrates at the active site of class I lysyl-tRNA synthetase.
  Biochemistry, 45, 3646-3652.  
15856481 J.Roach, S.Sharma, M.Kapustina, and C.W.Carter (2005).
Structure alignment via Delaunay tetrahedralization.
  Proteins, 60, 66-81.  
15845537 N.T.Uter, I.Gruic-Sovulj, and J.J.Perona (2005).
Amino acid-dependent transfer RNA affinity in a class I aminoacyl-tRNA synthetase.
  J Biol Chem, 280, 23966-23977.  
15840835 Y.Zhang, L.Wang, P.G.Schultz, and I.A.Wilson (2005).
Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine.
  Protein Sci, 14, 1340-1349.
PDB codes: 1u7d 1u7x
15096594 D.Y.Dubois, M.Blaise, H.D.Becker, V.Campanacci, G.Keith, R.Giegé, C.Cambillau, J.Lapointe, and D.Kern (2004).
An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNAAsp.
  Proc Natl Acad Sci U S A, 101, 7530-7535.  
15096612 J.C.Salazar, A.Ambrogelly, P.F.Crain, J.A.McCloskey, and D.Söll (2004).
A truncated aminoacyl-tRNA synthetase modifies RNA.
  Proc Natl Acad Sci U S A, 101, 7536-7541.  
15280378 J.Jia, X.L.Chen, L.T.Guo, Y.D.Yu, J.P.Ding, and Y.X.Jin (2004).
Residues Lys-149 and Glu-153 switch the aminoacylation of tRNA(Trp) in Bacillus subtilis.
  J Biol Chem, 279, 41960-41965.  
15561136 J.Lee, and T.L.Hendrickson (2004).
Divergent anticodon recognition in contrasting glutamyl-tRNA synthetases.
  J Mol Biol, 344, 1167-1174.  
14747465 J.Levengood, S.F.Ataide, H.Roy, and M.Ibba (2004).
Divergence in noncognate amino acid recognition between class I and class II lysyl-tRNA synthetases.
  J Biol Chem, 279, 17707-17714.  
15194701 L.Randau, S.Schauer, A.Ambrogelly, J.C.Salazar, J.Moser, S.Sekine, S.Yokoyama, D.Söll, and D.Jahn (2004).
tRNA recognition by glutamyl-tRNA reductase.
  J Biol Chem, 279, 34931-34937.  
15138304 M.Ibba, and C.Francklyn (2004).
Turning tRNA upside down: When aminoacylation is not a prerequisite to protein synthesis.
  Proc Natl Acad Sci U S A, 101, 7493-7494.  
15520379 M.R.Buddha, K.M.Keery, and B.R.Crane (2004).
An unusual tryptophanyl tRNA synthetase interacts with nitric oxide synthase in Deinococcus radiodurans.
  Proc Natl Acad Sci U S A, 101, 15881-15886.  
14764088 R.Banerjee, D.Y.Dubois, J.Gauthier, S.X.Lin, S.Roy, and J.Lapointe (2004).
The zinc-binding site of a class I aminoacyl-tRNA synthetase is a SWIM domain that modulates amino acid binding via the tRNA acceptor arm.
  Eur J Biochem, 271, 724-733.  
15489861 S.Hauenstein, C.M.Zhang, Y.M.Hou, and J.J.Perona (2004).
Shape-selective RNA recognition by cysteinyl-tRNA synthetase.
  Nat Struct Mol Biol, 11, 1134-1141.
PDB code: 1u0b
14999002 Y.Kaya, M.Del Campo, J.Ofengand, and A.Malhotra (2004).
Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold.
  J Biol Chem, 279, 18107-18110.
PDB code: 1si7
12737813 J.Cavarelli (2003).
Pushing induced fit to its limits: tRNA-dependent active site assembly in class I aminoacyl-tRNA synthetases.
  Structure, 11, 484-486.  
14690420 M.L.Bovee, M.A.Pierce, and C.S.Francklyn (2003).
Induced fit and kinetic mechanism of adenylation catalyzed by Escherichia coli threonyl-tRNA synthetase.
  Biochemistry, 42, 15102-15113.  
14690419 R.Geslain, G.Bey, J.Cavarelli, and G.Eriani (2003).
Limited set of amino acid residues in a class Ia aminoacyl-tRNA synthetase is crucial for tRNA binding.
  Biochemistry, 42, 15092-15101.  
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.