4G85

Crystal structure of human HisRS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.274 

wwPDB Validation 3D Report Full Report



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

  • DOI: 10.1016/j.str.2012.08.001
  • Structures With Same Primary Citation

  • 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 ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
Histidine-tRNA ligase, cytoplasmic
A, B
517Homo sapiensMutation(s): 0 
Gene Names: HARSHRSHARS1
EC: 6.1.1.21
Find proteins for P12081 (Homo sapiens)
Go to UniProtKB:  P12081
NIH Common Fund Data Resources
PHAROS  P12081
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.274 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.449α = 90
b = 100.449β = 90
c = 257.131γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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