1KMN

HISTIDYL-TRNA SYNTHETASE COMPLEXED WITH HISTIDINOL AND ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 

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This is version 1.3 of the entry. See complete history


Literature

The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase.

Arnez, J.G.Augustine, J.G.Moras, D.Francklyn, C.S.

(1997) Proc Natl Acad Sci U S A 94: 7144-7149

  • DOI: 10.1073/pnas.94.14.7144
  • Primary Citation of Related Structures:  
    1KMM, 1KMN

  • PubMed Abstract: 
  • The crystal structure of an enzyme-substrate complex with histidyl-tRNA synthetase from Escherichia coli, ATP, and the amino acid analog histidinol is described and compared with the previously obtained enzyme-product complex with histidyl-adenylate. An active site arginine, Arg-259, unique to all histidyl-tRNA synthetases, plays the role of the catalytic magnesium ion seen in seryl-tRNA synthetase ...

    The crystal structure of an enzyme-substrate complex with histidyl-tRNA synthetase from Escherichia coli, ATP, and the amino acid analog histidinol is described and compared with the previously obtained enzyme-product complex with histidyl-adenylate. An active site arginine, Arg-259, unique to all histidyl-tRNA synthetases, plays the role of the catalytic magnesium ion seen in seryl-tRNA synthetase. When Arg-259 is substituted with histidine, the apparent second order rate constant (kcat/Km) for the pyrophosphate exchange reaction and the aminoacylation reaction decreases 1,000-fold and 500-fold, respectively. Crystals soaked with MnCl2 reveal the existence of two metal binding sites between beta- and gamma-phosphates; these sites appear to stabilize the conformation of the pyrophosphate. The use of both conserved metal ions and arginine in phosphoryl transfer provides evidence of significant early functional divergence of class II aminoacyl-tRNA synthetases.


    Related Citations: 
    • Crystal Structure of Histidyl-tRNA Synthetase from Escherichia Coli Complexed with Histidyl-Adenylate
      Arnez, J.G., Harris, D.C., Mitschler, A., Rees, B., Francklyn, C.S., Moras, D.
      (1995) EMBO J 14: 4143
    • Crystallization of Histidyl-tRNA Synthetase from Escherichia Coli
      Francklyn, C., Harris, D., Moras, D.
      (1994) J Mol Biol 241: 275
    • Primary Structure of Histidine-tRNA Synthetase and Characterization of Hiss Transcripts
      Freedman, R., Gibson, B., Donovan, D., Biemann, K., Eisenbeis, S., Parker, J., Schimmel, P.
      (1985) J Biol Chem 260: 10063

    Organizational Affiliation

    Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale/Université Louis Pasteur, BP 163, 67404 Strasbourg-Illkirch, Cedex, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HISTIDYL-TRNA SYNTHETASEA, B, C, D424Escherichia coliMutation(s): 0 
EC: 6.1.1.21
UniProt
Find proteins for P60906 (Escherichia coli (strain K12))
Explore P60906 
Go to UniProtKB:  P60906
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60906
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.9α = 114.1
b = 107.3β = 97.4
c = 107.2γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MARXDSdata reduction
MARSCALEdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2015-06-24
    Changes: Non-polymer description