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: 101.03 kDa 
• Atom Count: 6205 
• Residue Count: 750 
• Unique protein chains: 1

1R6U

Crystal structure of an active fragment of human tryptophanyl-tRNA synthetase with cytokine activity

• DOI: 10.2210/pdb1R6U/pdb

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


• Deposited: 2003-10-16 Released: 2004-01-06 
• Deposition Author(s): Yang, X.-L., Otero, F.J., Skene, R.J., McRee, D.E., Ribas de Pouplana, L., Schimmel, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.297 
• R-Value Work: 0.254 
• R-Value Observed: 0.255 

Literature

Functional and crystal structure analysis of active site adaptations of a potent anti-angiogenic human tRNA synthetase

Yang, X.-L., Guo, M., Kapoor, M., Ewalt, K.L., Otero, F.J., Skene, R.J., McRee, D.E., Schimmel, P.

(2007) Structure 15: 793-805

• PubMed: 17637340 
• DOI: 10.1016/j.str.2007.05.009
• Primary Citation of Related Structures:  
  1R6U


• PubMed Abstract: 
  

Higher eukaryote tRNA synthetases have expanded functions that come from enlarged, more differentiated structures that were adapted to fit aminoacylation function. How those adaptations affect catalytic mechanisms is not known. Presented here is the structure of a catalytically active natural splice variant of human tryptophanyl-tRNA synthetase (TrpRS) that is a potent angiostatic factor. This and related structures suggest that a eukaryote-specific N-terminal extension of the core enzyme changed substrate recognition by forming an active site cap. At the junction of the extension and core catalytic unit, an arginine is recruited to replace a missing landmark lysine almost 200 residues away. Mutagenesis, rapid kinetic, and substrate binding studies support the functional significance of the cap and arginine recruitment. Thus, the enzyme function of human TrpRS has switched more to the N terminus of the sequence. This switch has the effect of creating selective pressure to retain the N-terminal extension for functional expansion.

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Organizational Affiliation: 

The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophanyl-tRNA synthetase	A, B	437	Homo sapiens	Mutation(s): 12  Gene Names: WARS, WARS1, IFI53, WRS 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TYM	A	TRYPTOPHANYL-5'AMP C21 H24 N7 O8 P IFQVDHDRFCKAAW-SQIXAUHQSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.297 
• R-Value Work: 0.254 
• R-Value Observed: 0.255 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.658	α = 90
b = 96.46	β = 129.9
c = 97.132	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-16 
• Released Date: 2004-01-06 
Deposition Author(s): Yang, X.-L., Otero, F.J., Skene, R.J., McRee, D.E., Ribas de Pouplana, L., Schimmel, P.

Revision History 

• Version 1.0: 2004-01-06
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance