PDBsum entry 2hrk

Go to PDB code: 
protein metals Protein-protein interface(s) links
Ligase/RNA binding protein PDB id
Protein chains
177 a.a. *
121 a.a. *
Waters ×274
* Residue conservation analysis
PDB id:
Name: Ligase/RNA binding protein
Title: Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub- complexes
Structure: Glutamyl-tRNA synthetase, cytoplasmic. Chain: a. Fragment: residues 1-207. Synonym: glutamate-tRNA ligase, glurs, p85. Engineered: yes. Gu4 nucleic-binding protein 1. Chain: b. Fragment: residues 1-122. Synonym: g4p1 protein, p42, arc1 protein.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: gus1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: arc1.
Biol. unit: Dimer (from PQS)
2.05Å     R-factor:   0.194     R-free:   0.256
Authors: H.Simader,D.Suck
Key ref: H.Simader et al. (2006). Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes. Nucleic Acids Res, 34, 3968-3979. PubMed id: 16914447 DOI: 10.1093/nar/gkl560
20-Jul-06     Release date:   05-Sep-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P46655  (SYEC_YEAST) -  Glutamate--tRNA ligase, cytoplasmic
708 a.a.
177 a.a.
Protein chain
Pfam   ArchSchema ?
P46672  (G4P1_YEAST) -  GU4 nucleic-binding protein 1
376 a.a.
121 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain A: E.C.  - Glutamate--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu)
+ L-glutamate
+ tRNA(Glu)
+ 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  


DOI no: 10.1093/nar/gkl560 Nucleic Acids Res 34:3968-3979 (2006)
PubMed id: 16914447  
Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes.
H.Simader, M.Hothorn, C.Köhler, J.Basquin, G.Simos, D.Suck.
The yeast aminoacyl-tRNA synthetase (aaRS) complex is formed by the methionyl- and glutamyl-tRNA synthetases (MetRS and GluRS, respectively) and the tRNA aminoacylation cofactor Arc1p. It is considered an evolutionary intermediate between prokaryotic aaRS and the multi- aaRS complex found in higher eukaryotes. While a wealth of structural information is available on the enzymatic domains of single aaRS, insight into complex formation between eukaryotic aaRS and associated protein cofactors is missing. Here we report crystal structures of the binary complexes between the interacting domains of Arc1p and MetRS as well as those of Arc1p and GluRS at resolutions of 2.2 and 2.05 A, respectively. The data provide a complete structural model for ternary complex formation between the interacting domains of MetRS, GluRS and Arc1p. The structures reveal that all three domains adopt a glutathione S-transferase (GST)-like fold and that simultaneous interaction of Arc1p with GluRS and MetRS is mediated by the use of a novel interface in addition to a classical GST dimerization interaction. The results demonstrate a novel role for this fold as a heteromerization domain specific to eukaryotic aaRS, associated proteins and protein translation elongation factors.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19932696 M.Guo, P.Schimmel, and X.L.Yang (2010).
Functional expansion of human tRNA synthetases achieved by structural inventions.
  FEBS Lett, 584, 434-442.  
20954242 S.Havrylenko, R.Legouis, B.Negrutskii, and M.Mirande (2010).
Methionyl-tRNA synthetase from Caenorhabditis elegans: a specific multidomain organization for convergent functional evolution.
  Protein Sci, 19, 2475-2484.  
20716358 V.Makarenkov, A.Boc, J.Xie, P.Peres-Neto, F.J.Lapointe, and P.Legendre (2010).
Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees.
  BMC Evol Biol, 10, 250.  
19417106 M.Frechin, B.Senger, M.Brayé, D.Kern, R.P.Martin, and H.D.Becker (2009).
Yeast mitochondrial Gln-tRNA(Gln) is generated by a GatFAB-mediated transamidation pathway involving Arc1p-controlled subcellular sorting of cytosolic GluRS.
  Genes Dev, 23, 1119-1130.  
18838389 J.Takeda, Y.Suzuki, R.Sakate, Y.Sato, M.Seki, T.Irie, N.Takeuchi, T.Ueda, M.Nakao, S.Sugano, T.Gojobori, and T.Imanishi (2008).
Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.
  Nucleic Acids Res, 36, 6386-6395.  
19000817 M.Guo, F.Xu, J.Yamada, T.Egelhofer, Y.Gao, G.A.Hartzog, M.Teng, and L.Niu (2008).
Core structure of the yeast spt4-spt5 complex: a conserved module for regulation of transcription elongation.
  Structure, 16, 1649-1658.  
18272479 M.Guo, M.Ignatov, K.Musier-Forsyth, P.Schimmel, and X.L.Yang (2008).
Crystal structure of tetrameric form of human lysyl-tRNA synthetase: Implications for multisynthetase complex formation.
  Proc Natl Acad Sci U S A, 105, 2331-2336.
PDB code: 3bju
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.