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PDBsum entry 2hra

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protein metals Protein-protein interface(s) links
Ligase PDB id
2hra
Jmol
Contents
Protein chains
180 a.a. *
Metals
IOD ×44
Waters ×271
* Residue conservation analysis
PDB id:
2hra
Name: Ligase
Title: Crystal structures of the interacting domains from yeast glu synthetase and tRNA aminoacylation and nuclear export cofac reveal a novel function for an old fold
Structure: Glutamyl-tRNA synthetase, cytoplasmic. Chain: a, b. Fragment: n-terminal heteromerisation domain, residues 1-20 synonym: glutamate-tRNA ligase, glurs, p85. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: gus1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.90Å     R-factor:   0.216     R-free:   0.262
Authors: H.Simader,M.Hothorn,D.Suck
Key ref:
H.Simader et al. (2006). Structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA-aminoacylation and nuclear-export cofactor Arc1p reveal a novel function for an old fold. Acta Crystallogr D Biol Crystallogr, 62, 1510-1519. PubMed id: 17139087 DOI: 10.1107/S0907444906039850
Date:
20-Jul-06     Release date:   05-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P46655  (SYEC_YEAST) -  Glutamate--tRNA ligase, cytoplasmic
Seq:
Struc:
 
Seq:
Struc:
708 a.a.
180 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
+ 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     tRNA aminoacylation   1 term 
  Biochemical function     nucleotide binding     3 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444906039850 Acta Crystallogr D Biol Crystallogr 62:1510-1519 (2006)
PubMed id: 17139087  
 
 
Structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA-aminoacylation and nuclear-export cofactor Arc1p reveal a novel function for an old fold.
H.Simader, M.Hothorn, D.Suck.
 
  ABSTRACT  
 
Eukaryotic aminoacyl-tRNA synthetases (aaRS) frequently contain additional appended domains that are absent from their prokaryotic counterparts which mediate complex formation between eukaryotic aaRS and cofactors of aminoacylation and translation. However, the structural basis of such interactions has remained elusive. The heteromerization domain of yeast glutamyl-tRNA synthetase (GluRS) has been cloned, expressed, purified and crystallized in space group C222(1), with unit-cell parameters a = 52, b = 107, c = 168 A. Phase information was obtained from multiple-wavelength anomalous dispersion with selenomethionine to 2.5 A resolution and the structure, comprising two monomers per asymmetric unit, was determined and refined to 1.9 A resolution. The structure of the interacting domain of its accessory protein Arc1p was determined and refined to 1.9 A resolution in a crystal form containing 20 monomers organized in five tetramers per asymmetric unit (space group C2, unit-cell parameters a = 222, b = 89, c = 127 A, beta = 99.4 degrees ). Both domains adopt a GST-like fold, demonstrating a novel role for this fold as a protein-protein interaction module.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 The structure of Arc1p-N contains 20 monomers organized in five tetramers per asymmetric unit. (a) The arrangement of the five tetramers (No. 1 in blue, 2 in green, 3 in red, 4 in cyan and 5 in yellow) in the unit cell. (b) The monomers within each tetramer are related by pseudo-twofold rotational symmetry and fall into three conformers (No. 1 in brown, 2 in green and 3 in grey) that differ by the orientation of their N-terminal -helix. The central frame in (b) indicates the section shown in detail in the supplementary material^1.
Figure 5.
Figure 5 Three suggested ways of interaction between GluRS-N and Arc1p-N. (a) Stereo representation of GluRS-N (blue/yellow) superimposed on conformer 1 (brown) of a Arc1p-N tetramer (color coding as in Fig. 3-b and 4-). Segments of GluRS-N corresponding to the interfacing elements of the E. coli GST homodimer are coloured yellow. (b) Analysis of GluRS-N surface conservation does not yield clues as to which area is likely to be involved in the GluRS-N-Arc1p-N interaction. Surface representations of GluRS-N are coloured in a white to green gradient corresponding to 10-90% sequence conservation (scoring by the Risler matrix; Risler et al., 1988[Risler, J. L., Delorme, M. O., Delacroix, H. & Henaut, A. (1988). J. Mol. Biol. 204, 1019-1029.]). The three views represent the three possible modes of interaction and are oriented and centred on the respective putative interface area: GST homodimer-like interaction (left), interaction corresponding to that indicated in (a) between GluRS-N and the grey Arc1p-N monomer (middle) and interaction corresponding to that indicated in (a) between GluRS-N and the green Arc1p-N monomer (right).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 1510-1519) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18522650 C.D.Hausmann, and M.Ibba (2008).
Aminoacyl-tRNA synthetase complexes: molecular multitasking revealed.
  FEMS Microbiol Rev, 32, 705-721.  
18343821 K.J.Kim, M.C.Park, S.J.Choi, Y.S.Oh, E.C.Choi, H.J.Cho, M.H.Kim, S.H.Kim, D.W.Kim, S.Kim, and B.S.Kang (2008).
Determination of three-dimensional structure and residues of the novel tumor suppressor AIMP3/p18 required for the interaction with ATM.
  J Biol Chem, 283, 14032-14040.
PDB code: 2uz8
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