1ADJ

HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/bi9618373
  • Primary Citation of Related Structures:  
  • Also Cited By: 1H4V

  • 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 cont ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTIDYL-TRNA SYNTHETASE
A, B, C, D
421Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: hisS
EC: 6.1.1.21
Find proteins for P56194 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P56194
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HIS
Query on HIS

Download SDF File 
Download CCD File 
A, B, C, D
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 171.300α = 90.00
b = 214.700β = 90.00
c = 49.300γ = 90.00
Software Package:
Software NamePurpose
CCP4data reduction
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-02-18 
  • Released Date: 1997-08-20 
  • Deposition Author(s): Cusack, S., Aberg, A.

Revision History 

  • Version 1.0: 1997-08-20
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance