Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 108.53 kDa 
• Atom Count: 6394 
• Residue Count: 760 
• Unique protein chains: 1

2QUH

Crystal structures of human tryptophanyl-tRNA synthetase in complex with Trp

• DOI: 10.2210/pdb2QUH/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-08-05 Released: 2008-04-29 
• Deposition Author(s): Shen, N., Ding, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.233 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 

Literature

Catalytic mechanism of the tryptophan activation reaction revealed by crystal structures of human tryptophanyl-tRNA synthetase in different enzymatic states

Shen, N., Zhou, M., Yang, B., Yu, Y., Dong, X., Ding, J.

(2008) Nucleic Acids Res 36: 1288-1299

• PubMed: 18180246 
• DOI: 10.1093/nar/gkm1153
• Primary Citation of Related Structures:  
  2QUK, 2QUJ, 2QUI, 2QUH


• PubMed Abstract: 
  

Human tryptophanyl-tRNA synthetase (hTrpRS) differs from its bacterial counterpart at several key positions of the catalytic active site and has an extra N-terminal domain, implying possibly a different catalytic mechanism. We report here the crystal structures of hTrpRS in complexes with Trp, tryptophanamide and ATP and tryptophanyl-AMP, respectively, which represent three different enzymatic states of the Trp activation reaction. Analyses of these structures reveal the molecular basis of the mechanisms of the substrate recognition and the activation reaction. The dimeric hTrpRS is structurally and functionally asymmetric with half-of-the-sites reactivity. Recognition of Trp is by an induced-fit mechanism involving conformational change of the AIDQ motif that creates a perfect pocket for the binding and activation of Trp and causes coupled movements of the N-terminal and C-terminal domains. The KMSAS loop appears to have an inherent flexibility and the binding of ATP stabilizes it in a closed conformation that secures the position of ATP for catalysis. Our structural data indicate that the catalytic mechanism of the Trp activation reaction by hTrpRS involves more moderate conformational changes of the structural elements at the active site to recognize and bind the substrates, which is more complex and fine-tuned than that of bacterial TrpRS.

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Organizational Affiliation: 

State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Graduate School of Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophanyl-tRNA synthetase	A, B	477	Homo sapiens	Mutation(s): 0  Gene Names: WARS, IFI53, WRS, WARS1 EC: 6.1.1.2
Find proteins for P23381 (Homo sapiens) Explore P23381  Go to UniProtKB:  P23381
NIH Common Fund Data Resources
PHAROS:  P23381 GTEx:  ENSG00000140105

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRP	B	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.233 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.9	α = 90
b = 79.9	β = 90
c = 382.3	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-08-05 
• Released Date: 2008-04-29 
Deposition Author(s): Shen, N., Ding, J.P.

Revision History 

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance