spacer
spacer
Go to PDB code: 
protein Protein-protein interface(s) links
Ligase PDB id
1qe0
Jmol
Contents
Protein chains
390 a.a. *
342 a.a. *
Waters ×100
* Residue conservation analysis
PDB id:
1qe0
Name: Ligase
Title: Crystal structure of apo s. Aureus histidyl-tRNA synthetase
Structure: Histidyl-tRNA synthetase. Chain: a, b. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.70Å     R-factor:   0.197     R-free:   0.270
Authors: X.Qiu,C.A.Janson,M.N.Blackburn,I.K.Chohan,M.Hibbs,S.S.Abdel- Meguid
Key ref:
X.Qiu et al. (1999). Cooperative structural dynamics and a novel fidelity mechanism in histidyl-tRNA synthetases. Biochemistry, 38, 12296-12304. PubMed id: 10493797 DOI: 10.1021/bi990482v
Date:
12-Jul-99     Release date:   12-Jul-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P60911  (SYH_STAAU) -  Histidyl-tRNA synthetase
Seq:
Struc: 		420 a.a.
390 a.a.*
Protein chain
Pfam   ArchSchema ?
P60911  (SYH_STAAU) -  Histidyl-tRNA synthetase
Seq:
Struc: 		420 a.a.
342 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.6.1.1.21  - Histidine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His)
ATP
 + L-histidine
 + tRNA(His)
 = AMP
 + diphosphate
 + L-histidyl-tRNA(His)
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   3 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi990482v Biochemistry 38:12296-12304 (1999)
PubMed id: 10493797  
 
 
Cooperative structural dynamics and a novel fidelity mechanism in histidyl-tRNA synthetases.
X.Qiu, C.A.Janson, M.N.Blackburn, I.K.Chhohan, M.Hibbs, S.S.Abdel-Meguid.
 
  ABSTRACT  
 
The crystal structure of the Staphylococcus aureus histidyl-tRNA synthetase apoprotein has been determined at 2.7 A resolution. Several important loops in the active site either become disordered or adopt very different conformations compared to their ligand-bound states. These include the histidine A motif (Arg257-Tyr262) that is essential for substrate recognition, a loop (Gly52-Lys62) that seems to control the communication between the histidine and ATP binding sites, the motif 2 loop (Glu114-Arg120) that binds ATP, and the insertion domain that is likely to bind tRNA. These ligand-induced structural changes are supported by fluorescence experiments, which also suggest highly cooperative dynamics. A dynamic and cooperative active site is most likely necessary for the proper functioning of the histidyl-tRNA synthetase, and suggests a novel mechanism for improving charging fidelity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21419778 D.Anunciado, A.Dhar, M.Gruebele, and A.M.Baranger (2011).
Multistep kinetics of the U1A-SL2 RNA complex dissociation.
  J Mol Biol, 408, 896-908.  
20132829 E.A.Merritt, T.L.Arakaki, J.R.Gillespie, E.T.Larson, A.Kelley, N.Mueller, A.J.Napuli, J.Kim, L.Zhang, C.L.Verlinde, E.Fan, F.Zucker, F.S.Buckner, W.C.van Voorhis, and W.G.Hol (2010).
Crystal structures of trypanosomal histidyl-tRNA synthetase illuminate differences between eukaryotic and prokaryotic homologs.
  J Mol Biol, 397, 481-494.
PDB codes: 3hri 3hrk 3lc0
19487703 E.Guth, M.Farris, M.Bovee, and C.S.Francklyn (2009).
Asymmetric amino acid activation by class II histidyl-tRNA synthetase from Escherichia coli.
  J Biol Chem, 284, 20753-20762.  
18850722 C.S.Francklyn (2008).
DNA polymerases and aminoacyl-tRNA synthetases: shared mechanisms for ensuring the fidelity of gene expression.
  Biochemistry, 47, 11695-11703.  
16051603 K.S.Champagne, M.Sissler, Y.Larrabee, S.Doublié, and C.S.Francklyn (2005).
Activation of the hetero-octameric ATP phosphoribosyl transferase through subunit interface rearrangement by a tRNA synthetase paralog.
  J Biol Chem, 280, 34096-34104.
PDB codes: 1z7m 1z7n
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.  
12787471 S.J.Hughes, J.A.Tanner, A.D.Hindley, A.D.Miller, and I.R.Gould (2003).
Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment.
  BMC Struct Biol, 3, 5.  
12458790 C.Francklyn, J.J.Perona, J.Puetz, and Y.M.Hou (2002).
Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation.
  RNA, 8, 1363-1372.  
11076509 J.D.Colandene, and M.D.Topal (2000).
Evidence for mutations that break communication between the Endo and Topo domains in NaeI endonuclease/topoisomerase.
  Biochemistry, 39, 13703-13707.  
10966471 M.Ibba, and D.Soll (2000).
Aminoacyl-tRNA synthesis.
  Annu Rev Biochem, 69, 617-650.  
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.