4TVA

Universal Pathway for Post-Transfer Editing Reactions: Insight from Crystal structure of TthPheRS with Puromycine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 

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Literature

Universal pathway for posttransfer editing reactions: Insights from the crystal structure of TtPheRS with puromycin.

Tworowski, D., Klipcan, L., Peretz, M., Moor, N., Safro, M.G.

(2015) Proc Natl Acad Sci U S A 112: 3967-3972

  • DOI: 10.1073/pnas.1414852112
  • Primary Citation of Related Structures:  
    4TVA

  • PubMed Abstract: 

    • At the amino acid binding and recognition step, phenylalanyl-tRNA synthetase (PheRS) faces the challenge of discrimination between cognate phenylalanine and closely similar noncognate tyrosine. Resampling of Tyr-tRNA(Phe) to PheRS increasing the number of correctly charged tRNA molecules has recently been revealed ...

    At the amino acid binding and recognition step, phenylalanyl-tRNA synthetase (PheRS) faces the challenge of discrimination between cognate phenylalanine and closely similar noncognate tyrosine. Resampling of Tyr-tRNA(Phe) to PheRS increasing the number of correctly charged tRNA molecules has recently been revealed. Thus, the very same editing site of PheRS promotes hydrolysis of misacylated tRNA species, associated both with cis- and trans-editing pathways. Here we report the crystal structure of Thermus thermophilus PheRS (TtPheRS) at 2.6 Å resolution, in complex with phenylalanine and antibiotic puromycin mimicking the A76 of tRNA acylated with tyrosine. Starting from the complex structure and using a hybrid quantum mechanics/molecular mechanics approach, we investigate the pathways of editing reaction catalyzed by TtPheRS. We show that both 2' and 3' isomeric esters undergo mutual transformation via the cyclic intermediate orthoester, and the editing site can readily accommodate a model of Tyr-tRNA(Phe) where deacylation occurs from either the 2'- or 3'-OH. The suggested pathway of the hydrolytic reaction at the editing site of PheRS is of sufficient generality to warrant comparison with other class I and class II aminoacyl-tRNA synthetases.

    Organizational Affiliation: 

    Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; mark.safro@weizmann.ac.il.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phenylalanine--tRNA ligase alpha subunitA350Thermus thermophilusMutation(s): 0 
Gene Names: pheS
EC: 6.1.1.20
UniProt
Find proteins for P27001 (Thermus thermophilus)
Explore P27001 
Go to UniProtKB:  P27001
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27001
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phenylalanine--tRNA ligase beta subunitB785Thermus thermophilusMutation(s): 0 
EC: 6.1.1.20
UniProt
Find proteins for Q5SGX1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SGX1 
Go to UniProtKB:  Q5SGX1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SGX1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PUY
Query on PUY
Download Ideal Coordinates CCD File 
D [auth B]PUROMYCIN
C22 H29 N7 O5
RXWNCPJZOCPEPQ-NVWDDTSBSA-N		 Ligand Interaction
PHE
Query on PHE
Download Ideal Coordinates CCD File 
C [auth A]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.475α = 90
b = 173.475β = 90
c = 138.492γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Database references
  • Version 1.2: 2015-04-15
    Changes: Database references
  • Version 1.3: 2015-10-07
    Changes: Experimental preparation