1KMN

HISTIDYL-TRNA SYNTHETASE COMPLEXED WITH HISTIDINOL AND ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


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.USA 94: 7144-7149

  • Primary Citation of Related Structures:  

  • 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. ...

    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: 
    • 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
    • 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


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTIDYL-TRNA SYNTHETASE
A, B, C, D
424Escherichia coli (strain K12)Gene Names: hisS
EC: 6.1.1.21
Find proteins for P60906 (Escherichia coli (strain K12))
Go to UniProtKB:  P60906
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C, D
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
HSO
Query on HSO

Download SDF File 
Download CCD File 
A, B, C, D
L-histidinol
C6 H12 N3 O
ZQISRDCJNBUVMM-YFKPBYRVSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.249 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 60.900α = 114.10
b = 107.300β = 97.40
c = 107.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
MARSCALEdata scaling
MARXDSdata reduction
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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