4KQE | pdb_00004kqe

The mutant structure of the human glycyl-tRNA synthetase E71G

• PDB DOI: https://doi.org/10.2210/pdb4KQE/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-15 Released: 2014-05-21 
• Deposition Author(s): Qin, X., Hao, Z., Tian, Q., Zhang, Z., Zhou, C., Xie, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 
  0.255 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Large Conformational Changes of Insertion 3 in Human Glycyl-tRNA Synthetase (hGlyRS) during Catalysis

Deng, X., Qin, X., Chen, L., Jia, Q., Zhang, Y., Zhang, Z., Lei, D., Ren, G., Zhou, Z., Wang, Z., Li, Q., Xie, W.

(2016) J Biological Chem 291: 5740-5752

• PubMed: 26797133 
• DOI: https://doi.org/10.1074/jbc.M115.679126
• Primary Citation Related Structures: 
  4KQE, 4QEI


• PubMed Abstract: 
  

  Glycyl-tRNA synthetase (GlyRS) is the enzyme that covalently links glycine to cognate tRNA for translation. It is of great research interest because of its nonconserved quaternary structures, unique species-specific aminoacylation properties, and noncanonical functions in neurological diseases, but none of these is fully understood. We report two crystal structures of human GlyRS variants, in the free form and in complex with tRNA(Gly) respectively, and reveal new aspects of the glycylation mechanism. We discover that insertion 3 differs considerably in conformation in catalysis and that it acts like a "switch" and fully opens to allow tRNA to bind in a cross-subunit fashion. The flexibility of the protein is supported by molecular dynamics simulation, as well as enzymatic activity assays. The biophysical and biochemical studies suggest that human GlyRS may utilize its flexibility for both the traditional function (regulate tRNA binding) and alternative functions (roles in diseases).

---

Organizational Affiliation: 
• From the State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China,; the Center for Cellular and Structural Biology and.
the South China Sea Institute, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.
the Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China, and.
the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720.
the Center for Cellular and Structural Biology and; the School of Pharmaceutical Sciences, Sun Yat-Sen University, University City, Guangzhou, Guangdong 510006, China.
From the State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China,; the Center for Cellular and Structural Biology and. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 78.72 kDa 
• Atom Count: 4,756 
• Modeled Residue Count: 597 
• Deposited Residue Count: 693 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine--tRNA ligase	A	693	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free:  0.255 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.239	α = 90
b = 91.239	β = 90
c = 246.614	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-21 
Deposition Author(s): Qin, X., Hao, Z., Tian, Q., Zhang, Z., Zhou, C., Xie, W.

Revision History  

• Version 1.0: 2014-05-21
  Type: Initial release
  
• Version 1.1: 2014-05-28
  Changes: Database references
• Version 1.2: 2016-04-13
  Changes: Database references, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description