Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 109.47 kDa 
• Atom Count: 6778 
• Modelled Residue Count: 802 
• Deposited Residue Count: 954 
• Unique protein chains: 1

1R6T

crystal structure of human tryptophanyl-tRNA synthetase

• PDB DOI: 10.2210/pdb1R6T/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: 2.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains

Yang, X.-L., Otero, F.J., Skene, R.J., McRee, D.E., Schimmel, P., Ribas De Pouplana, L.

(2003) Proc Natl Acad Sci U S A 100: 15376-15380

• PubMed: 14671330 
• DOI: 10.1073/pnas.2136794100
• Primary Citation of Related Structures:  
  1Q11, 1R6T


• PubMed Abstract: 
  

Early forms of the genetic code likely generated "statistical" proteins, with similar side chains occupying the same sequence positions at different ratios. In this scenario, groups of related side chains were treated by aminoacyl-tRNA synthetases as a single molecular species until a discrimination mechanism developed that could separate them. The aromatic amino acids tryptophan, tyrosine, and phenylalanine likely constituted one of these groups. A crystal structure of human tryptophanyl-tRNA synthetase was solved at 2.1 A with a tryptophanyl-adenylate bound at the active site. A cocrystal structure of an active fragment of human tyrosyl-tRNA synthetase with its cognate amino acid analog was also solved at 1.6 A. The two structures enabled active site identifications and provided the information for structure-based sequence alignments of approximately 45 orthologs of each enzyme. Two critical positions shared by all tyrosyl-tRNA synthetases and tryptophanyl-tRNA synthetases for amino acid discrimination were identified. The variations at these two positions and phylogenetic analyses based on the structural information suggest that, in contrast to many other amino acids, discrimination of tyrosine from tryptophan occurred late in the development of the genetic code.

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Organizational Affiliation: 

Departments of Molecular Biology and Chemistry, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophanyl-tRNA synthetase	A, B	477	Homo sapiens	Mutation(s): 14  Gene Names: WARS, WARS1, IFI53, WRS EC: 6.1.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for P23381 (Homo sapiens) Explore P23381  Go to UniProtKB:  P23381
PHAROS:  P23381

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TYM	C [auth A]	TRYPTOPHANYL-5'AMP C21 H24 N7 O8 P IFQVDHDRFCKAAW-SQIXAUHQSA-N
GOL	D [auth A], E [auth B]	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: 2.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.146	α = 90
b = 95.713	β = 91.62
c = 98.506	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
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations