4KR2

Glycyl-tRNA synthetase in complex with tRNA-Gly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Cocrystal Structures of Glycyl-tRNA Synthetase in Complex with tRNA Suggest Multiple Conformational States in Glycylation

Qin, X.Hao, Z.Tian, Q.Zhang, Z.Zhou, C.Xie, W.

(2014) J Biol Chem 289: 20359-20369

  • DOI: https://doi.org/10.1074/jbc.M114.557249
  • Primary Citation of Related Structures:  
    4KR2, 4KR3

  • PubMed Abstract: 

    Aminoacyl-tRNA synthetases are an ancient enzyme family that specifically charges tRNA molecules with cognate amino acids for protein synthesis. Glycyl-tRNA synthetase (GlyRS) is one of the most intriguing aminoacyl-tRNA synthetases due to its divergent quaternary structure and abnormal charging properties. In the past decade, mutations of human GlyRS (hGlyRS) were also found to be associated with Charcot-Marie-Tooth disease. However, the mechanisms of traditional and alternative functions of hGlyRS are poorly understood due to a lack of studies at the molecular basis. In this study we report crystal structures of wild type and mutant hGlyRS in complex with tRNA and with small substrates and describe the molecular details of enzymatic recognition of the key tRNA identity elements in the acceptor stem and the anticodon loop. The cocrystal structures suggest that insertions 1 and 3 work together with the active site in a cooperative manner to facilitate efficient substrate binding. Both the enzyme and tRNA molecules undergo significant conformational changes during glycylation. A working model of multiple conformations for hGlyRS catalysis is proposed based on the crystallographic and biochemical studies. This study provides insights into the catalytic pathway of hGlyRS and may also contribute to our understanding of Charcot-Marie-Tooth disease.


  • Organizational Affiliation

    From the Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou 510275, China, Center for Cellular and Structural Biology, The Sun Yat-Sen University, 132 E. Circle, University City, Guangzhou 510006, China, and.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycine--tRNA ligase637Homo sapiensMutation(s): 0 
Gene Names: GARS
EC: 6.1.1.14 (PDB Primary Data), 2.7.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P41250 (Homo sapiens)
Explore P41250 
Go to UniProtKB:  P41250
PHAROS:  P41250
GTEx:  ENSG00000106105 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41250
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
Gly-tRNA-CCCB [auth C]74Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.964α = 90
b = 88.499β = 90
c = 80.497γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description