Biological Assembly 1  

 3D View: Structure | Electron Density

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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: 116858.69 
• Atom Count: 6432 
• Residue Count: 1034 
• Unique protein chains: 1

4G85

Crystal structure of human HisRS

• DOI: 10.2210/pdb4G85/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2012-07-21 Released: 2012-09-26 
• Deposition Author(s): Wei, Z., Wu, J., Zhou, J.J., Yang, X.-L., Zhang, M., Schimmel, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 0.327 
• R-Value Work: 0.271 

Literature

Internally Deleted Human tRNA Synthetase Suggests Evolutionary Pressure for Repurposing.

Xu, Z., Wei, Z., Zhou, J.J., Ye, F., Lo, W.S., Wang, F., Lau, C.F., Wu, J., Nangle, L.A., Chiang, K.P., Yang, X.L., Zhang, M., Schimmel, P.

(2012) Structure 20: 1470-1477

• PubMed: 22958643 
• DOI: 10.1016/j.str.2012.08.001
• Primary Citation of Related Structures:  
  4G84


• PubMed Abstract: 
  

Aminoacyl-tRNA synthetases (AARSs) catalyze aminoacylation of tRNAs in the cytoplasm. Surprisingly, AARSs also have critical extracellular and nuclear functions. Evolutionary pressure for new functions might be manifested by splice variants that skip only an internal catalytic domain (CD) and link noncatalytic N- and C-terminal polypeptides. Using disease-associated histidyl-tRNA synthetase (HisRS) as an example, we found an expressed 171-amino acid protein (HisRSΔCD) that deleted the entire CD, and joined an N-terminal WHEP to the C-terminal anticodon-binding domain (ABD). X-ray crystallography and three-dimensional NMR revealed the structures of human HisRS and HisRSΔCD. In contrast to homodimeric HisRS, HisRSΔCD is monomeric, where rupture of the ABD's packing with CD resulted in a dumbbell-like structure of flexibly linked WHEP and ABD domains. In addition, the ABD of HisRSΔCD presents a distinct local conformation. This natural internally deleted HisRS suggests evolutionary pressure to reshape AARS tertiary and quaternary structures for repurposing.

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Organizational Affiliation: 

IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histidine-tRNA ligase, cytoplasmic	A, B	517	Homo sapiens	Mutation(s): 0  Gene Names: HARS (HRS) EC: 6.1.1.21
Find proteins for P12081 (Homo sapiens) Go to Gene View: HARS Go to UniProtKB:  P12081

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 0.327 
• R-Value Work: 0.271 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 100.449	α = 90.00
b = 100.449	β = 90.00
c = 257.131	γ = 90.00

Software Package:

Software Name	Purpose
ADSC	data collection
HKL-2000	data reduction
PHASER	phasing
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-21 
• Released Date: 2012-09-26 
• Deposition Author(s): Wei, Z., Wu, J., Zhou, J.J., Yang, X.-L., Zhang, M., Schimmel, P.

Revision History 

• Version 1.0: 2012-09-26
  Type: Initial release