5UD5

Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase bound to tRNA(Pyl)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.347 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase.

Suzuki, T.Miller, C.Guo, L.T.Ho, J.M.L.Bryson, D.I.Wang, Y.S.Liu, D.R.Soll, D.

(2017) Nat. Chem. Biol. 13: 1261-1266

  • DOI: 10.1038/nchembio.2497
  • Primary Citation of Related Structures:  5V6X

  • PubMed Abstract: 
  • Pyrrolysyl-tRNA synthetase (PylRS) is a major tool in genetic code expansion using noncanonical amino acids, yet its structure and function are not completely understood. Here we describe the crystal structure of the previously uncharacterized essent ...

    Pyrrolysyl-tRNA synthetase (PylRS) is a major tool in genetic code expansion using noncanonical amino acids, yet its structure and function are not completely understood. Here we describe the crystal structure of the previously uncharacterized essential N-terminal domain of this unique enzyme in complex with tRNAPyl. This structure explains why PylRS remains orthogonal in a broad range of organisms, from bacteria to humans. The structure also illustrates why tRNAPyl recognition by PylRS is anticodon independent: the anticodon does not contact the enzyme. Then, using standard microbiological culture equipment, we established a new method for laboratory evolution-a noncontinuous counterpart of the previously developed phage-assisted continuous evolution. With this method, we evolved novel PylRS variants with enhanced activity and amino acid specificity. Finally, we employed an evolved PylRS variant to determine its N-terminal domain structure and show how its mutations improve PylRS activity in the genetic encoding of a noncanonical amino acid.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyrrolysine--tRNA ligase
A, B
109Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)Gene Names: pylS
EC: 6.1.1.26
Find proteins for Q8PWY1 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Go to UniProtKB:  Q8PWY1
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (70-MER)C,D72Methanosarcina mazei Go1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.347 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.216 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.280α = 90.00
b = 72.280β = 90.00
c = 238.970γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-12-23 
  • Released Date: 2017-10-11 
  • Deposition Author(s): Suzuki, T., Soll, D.

Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM22854

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references
  • Version 1.2: 2017-11-01
    Type: Database references
  • Version 1.3: 2017-12-06
    Type: Database references