3VQY

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and AMPPNP (form 2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

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This is version 1.2 of the entry. See complete history


Literature

A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site

Yanagisawa, T.Sumida, T.Ishii, R.Yokoyama, S.

(2013) Acta Crystallogr D Biol Crystallogr 69: 5-15

  • DOI: https://doi.org/10.1107/S0907444912039881
  • Primary Citation of Related Structures:  
    3VQV, 3VQW, 3VQX, 3VQY

  • PubMed Abstract: 

    Structures of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) have been determined in a novel crystal form. The triclinic form crystals contained two PylRS dimers (four monomer molecules) in the asymmetric unit, in which the two subunits in one dimer each bind N(ℇ)-(tert-butyloxycarbonyl)-L-lysyladenylate (BocLys-AMP) and the two subunits in the other dimer each bind AMP. The BocLys-AMP molecules adopt a curved conformation and the C(α) position of BocLys-AMP protrudes from the active site. The β7-β8 hairpin structures in the four PylRS molecules represent distinct conformations of different states of the aminoacyl-tRNA synthesis reaction. Tyr384, at the tip of the β7-β8 hairpin, moves from the edge to the inside of the active-site pocket and adopts multiple conformations in each state. Furthermore, a new crystal structure of the BocLys-AMPPNP-bound form is also reported. The bound BocLys adopts an unusually bent conformation, which differs from the previously reported structure. It is suggested that the present BocLys-AMPPNP-bound, BocLys-AMP-bound and AMP-bound complexes represent the initial binding of an amino acid (or pre-aminoacyl-AMP synthesis), pre-aminoacyl-tRNA synthesis and post-aminoacyl-tRNA synthesis states, respectively. The conformational changes of Asn346 that accompany the aminoacyl-tRNA synthesis reaction have been captured by X-ray crystallographic analyses. The orientation of the Asn346 side chain, which hydrogen-bonds to the carbonyl group of the amino-acid substrate, shifts by a maximum of 85-90° around the C(β) atom.


  • Organizational Affiliation

    RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrrolysine--tRNA ligase291Methanosarcina mazeiMutation(s): 0 
Gene Names: pylS
EC: 6.1.1.26
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.355α = 90
b = 103.355β = 90
c = 70.906γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description