2ZIO

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Multistep Engineering of Pyrrolysyl-tRNA Synthetase to Genetically Encode N(varepsilon)-(o-Azidobenzyloxycarbonyl) lysine for Site-Specific Protein Modification

Yanagisawa, T.Ishii, R.Fukunaga, R.Kobayashi, T.Sakamoto, K.Yokoyama, S.

(2008) Chem.Biol. 15: 1187-1197

  • DOI: 10.1016/j.chembiol.2008.10.004
  • Primary Citation of Related Structures:  2ZIN

  • PubMed Abstract: 
  • Pyrrolysyl-tRNA synthetase (PylRS) esterifies pyrrolysine to tRNA(Pyl). In this study, N(epsilon)-(tert-butyloxycarbonyl)-L-lysine (BocLys) and N(epsilon)-allyloxycarbonyl-L-lysine (AlocLys) were esterified to tRNA(Pyl) by PylRS. Crystal structures o ...

    Pyrrolysyl-tRNA synthetase (PylRS) esterifies pyrrolysine to tRNA(Pyl). In this study, N(epsilon)-(tert-butyloxycarbonyl)-L-lysine (BocLys) and N(epsilon)-allyloxycarbonyl-L-lysine (AlocLys) were esterified to tRNA(Pyl) by PylRS. Crystal structures of a PylRS catalytic fragment complexed with BocLys and an ATP analog and with AlocLys-AMP revealed that PylRS requires an N(epsilon)-carbonyl group bearing a substituent with a certain size. A PylRS(Y384F) mutant obtained by random screening exhibited higher in vitro aminoacylation and in vivo amber suppression activities with BocLys, AlocLys, and pyrrolysine than those of the wild-type PylRS. Furthermore, the structure-based Y306A mutation of PylRS drastically increased the in vitro aminoacylation activity for N(epsilon)-benzyloxycarbonyl-L-lysine (ZLys). A PylRS with both the Y306A and Y384F mutations enabled the large-scale preparation (>10 mg per liter medium) of proteins site-specifically containing N(epsilon)-(o-azidobenzyloxycarbonyl)-L-lysine (AzZLys). The AzZLys-containing protein was labeled with a fluorescent probe, by Staudinger ligation.


    Organizational Affiliation

    Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyrrolysyl-tRNA synthetase
A
291Methanosarcina 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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AYB
Query on AYB

Download SDF File 
Download CCD File 
A
5'-O-[(S)-({(2S)-2-amino-6-[(propoxycarbonyl)amino]hexanoyl}oxy)(hydroxy)phosphoryl]adenosine
NE-ALLYLOXYCARBONYL-L-LYSINE-5'-ADENOSINE MONOPHOSPHATE
C20 H32 N7 O10 P
FNGSPKAFCIGHDI-URQYDQELSA-N
 Ligand Interaction
2PN
Query on 2PN

Download SDF File 
Download CCD File 
A
IMIDODIPHOSPHORIC ACID
H5 N O6 P2
GNGSOPFGGKKDQP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 104.150α = 90.00
b = 104.150β = 90.00
c = 71.060γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
MOLREPphasing
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance