Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.260 

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Crystal structure analysis of the activation of histidine by Thermus thermophilus histidyl-tRNA synthetase.

Aberg, A.Yaremchuk, A.Tukalo, M.Rasmussen, B.Cusack, S.

(1997) Biochemistry 36: 3084-3094

  • DOI: https://doi.org/10.1021/bi9618373
  • Primary Citation of Related Structures:  
    1ADJ, 1ADY

  • PubMed Abstract: 

    The crystal structure at 2.7 A resolution of histidyl-tRNA synthetase (HisRS) from Thermus thermophilus in complex with its amino acid substrate histidine has been determined. In the crystal asymmetric unit there are two homodimers, each subunit containing 421 amino acid residues. Each monomer of the enzyme consists of three domains: (1) an N-terminal catalytic domain containing a six-stranded antiparallel beta-sheet and the three motifs common to all class II aminoacyl-tRNA synthetases, (2) a 90-residue C-terminal alpha/beta domain which is common to most class IIa synthetases and is probably involved in recognizing the anticodon stem-loop of tRNA(His), and (3) a HisRS-specific alpha-helical domain inserted into the catalytic domain, between motifs II and III. The position of the insertion domain above the catalytic site suggests that it could clamp onto the acceptor stem of the tRNA during aminoacylation. Two HisRS-specific peptides, 259-RGLDYY and 285-GGRYDG, are intimately involved in forming the binding site for the histidine, a molecule of which is found in the active site of each monomer. The structure of HisRS in complex with histidyl adenylate, produced enzymatically in the crystal, has been determined at 3.2 A resolution. This structure shows that the HisRS-specific Arg-259 interacts directly with the alpha-phosphate of the adenylate on the opposite side to the usual conserved motif 2 arginine. Arg-259 thus substitutes for the divalent cation observed in seryl-tRNA synthetase and plays a crucial catalytic role in the mechanism of histidine activation.

  • Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
421Thermus thermophilusMutation(s): 0 
Find proteins for P56194 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P56194 
Go to UniProtKB:  P56194
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56194
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.260 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.3α = 90
b = 214.7β = 90
c = 49.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-08-20
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-04-03
    Changes: Refinement description