7R6O | pdb_00007r6o

Pyrrolysyl-tRNA synthetase from methanogenic archaeon ISO4-G1 (G1PylRS)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.269 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7R6O

This is version 1.2 of the entry. See complete history

Literature

Genetic Encoding of Cyanopyridylalanine for In-Cell Protein Macrocyclization by the Nitrile-Aminothiol Click Reaction.

Abdelkader, E.H.Qianzhu, H.George, J.Frkic, R.L.Jackson, C.J.Nitsche, C.Otting, G.Huber, T.

(2022) Angew Chem Int Ed Engl 61: e202114154-e202114154

  • DOI: https://doi.org/10.1002/anie.202114154
  • Primary Citation Related Structures: 
    7R6O

  • PubMed Abstract: 

    Cyanopyridylalanines are non-canonical amino acids that react with aminothiol compounds under physiological conditions in a biocompatible manner without requiring added catalyst. Here we present newly developed aminoacyl-tRNA synthetases for genetic encoding of meta- and para-cyanopyridylalanine to enable the site-specific attachment of a wide range of different functionalities. The outstanding utility of the cyanopyridine moiety is demonstrated by examples of i) post-translational functionalization of proteins, ii) in-cell macrocyclization of peptides and proteins, and iii) protein stapling. The biocompatible nature of the protein ligation chemistry enabled by the cyanopyridylalanine amino acid opens a new path to specific in vivo protein modifications in complex biological environments.


  • Organizational Affiliation
    • ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.

Macromolecule Content 

  • Total Structure Weight: 123.85 kDa 
  • Atom Count: 9,301 
  • Modeled Residue Count: 1,092 
  • Deposited Residue Count: 1,092 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pyrrolysyl-tRNA synthetase PylS
A, B, C, D
273methanogenic archaeon mixed culture ISO4-G1Mutation(s): 0 
Gene Names: AUP07_0651
UniProt
Find proteins for A0ACD6B8V0 (methanogenic archaeon mixed culture ISO4-G1)
Explore A0ACD6B8V0 
Go to UniProtKB:  A0ACD6B8V0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B8V0
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.269 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.855α = 90
b = 81.348β = 102.142
c = 121.845γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP200100348
Australian Research Council (ARC)AustraliaDP21010088

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-03-30
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description