5ZDL

Crystal Structure Analysis of TtQRS in co-crystallised with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.227 

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Ligand Structure Quality Assessment 


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Literature

Structural and functional analysis of Glutaminyl-tRNA synthetase (TtGlnRS) from Thermus thermophilus HB8 and its complexes

Nachiappan, M.Jain, V.Sharma, A.Yogavel, M.Jeyakanthan, J.

(2018) Int J Biol Macromol 120: 1379-1386

  • DOI: 10.1016/j.ijbiomac.2018.09.115
  • Primary Citation of Related Structures:  
    5ZDO, 5ZDL, 5ZDK

  • PubMed Abstract: 
  • Aminoacyl-tRNA synthetases (AaRSs) are vital enzymes for translation of proteins in cells. AaRSs catalyse the esterification of a specific amino acid to corresponding tRNAs to form an aminoacyl-tRNA that is used in ribosome-based protein synthesis. We focused on Glutaminyl tRNA synthetase (GlnRS) enzyme from the extreme thermophile Thermus thermophilus for structural studies ...

    Aminoacyl-tRNA synthetases (AaRSs) are vital enzymes for translation of proteins in cells. AaRSs catalyse the esterification of a specific amino acid to corresponding tRNAs to form an aminoacyl-tRNA that is used in ribosome-based protein synthesis. We focused on Glutaminyl tRNA synthetase (GlnRS) enzyme from the extreme thermophile Thermus thermophilus for structural studies. Our thermal shift assays show binding of enzyme substrates L-Gln and ATP as well as of various metals including cesium. We resolved crystal structures of apo-GlnRS as well as those in complex with AMP and ATP at 2.8 Å, 2.4 Å and 2.6 Å respectively. The bound cesium was found at the site of magnesium that typically binds to GlnRS. High structural conservation was evident in the Thermus thermophilus GlnRS when compared to those from Escherichia coli GlnRS.


    Organizational Affiliation

    Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 003, India. Electronic address: jjkanthan@gmail.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamine--tRNA ligaseA548Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA0549
EC: 6.1.1.18
UniProt
Find proteins for Q5SKU4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKU4 
Go to UniProtKB:  Q5SKU4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.084α = 90
b = 39.363β = 116.8
c = 114.846γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
AMoREphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release