4G84 | pdb_00004g84

Crystal structure of human HisRS

• PDB DOI: https://doi.org/10.2210/pdb4G84/pdb

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


• 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: 2.40 Å
• R-Value Free: 
  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1016/j.str.2012.08.001
• Primary Citation Related Structures: 
  4G84, 4G85


• 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.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 105.26 kDa 
• Atom Count: 7,094 
• Modeled Residue Count: 871 
• Deposited Residue Count: 928 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine--tRNA ligase, cytoplasmic	A, B	464	Homo sapiens	Mutation(s): 0  Gene Names: HARS, HRS EC: 6.1.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for P12081 (Homo sapiens) Explore P12081  Go to UniProtKB:  P12081
PHAROS:  P12081 GTEx:  ENSG00000170445

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	C [auth A], D [auth B], E [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CL	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.519	α = 90
b = 93.519	β = 90
c = 254.533	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description