5K1P

Catalytic domain of polyspecific pyrrolysyl-tRNA synthetase mutant N346A/C348A in complex with AMPPNP

  • Classification: LIGASE
  • Organism(s): Methanosarcina mazei
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2016-05-18 Released: 2016-10-19 
  • Deposition Author(s): Weber, A.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Science Foundation (NSF, United States), Welch Foundation, German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Genetically encoded fluorophenylalanines enable insights into the recognition of lysine trimethylation by an epigenetic reader.

Lee, Y.J., Schmidt, M.J., Tharp, J.M., Weber, A., Koenig, A.L., Zheng, H., Gao, J., Waters, M.L., Summerer, D., Liu, W.R.

(2016) Chem Commun (Camb) 52: 12606-12609

  • DOI: https://doi.org/10.1039/c6cc05959g
  • Primary Citation of Related Structures:  
    5K1P, 5K1X

  • PubMed Abstract: 

    Fluorophenylalanines bearing 2-5 fluorine atoms at the phenyl ring have been genetically encoded by amber codon. Replacement of F59, a phenylalanine residue that is directly involved in interactions with trimethylated K9 of histone H3, in the Mpp8 chromodomain recombinantly with fluorophenylalanines significantly impairs the binding to a K9-trimethylated H3 peptide.

    • Organizational Affiliation: 

    Department of Chemistry, Texas A&M University, College Station, TX 7743, USA. wliu@chem.tamu.edu.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrrolysine--tRNA ligase274Methanosarcina mazeiMutation(s): 2 
Gene Names: pylS, MM_1445
EC: 6.1.1.26
UniProt
Find proteins for Q8PWY1 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q8PWY1 
Go to UniProtKB:  Q8PWY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PWY1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.493α = 90
b = 44.358β = 99.92
c = 64.314γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

  • Released Date: 2016-10-19 
    • Deposition Author(s): Weber, A.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA161158
National Science Foundation (NSF, United States)United StatesCHEM-1148684
Welch FoundationUnited StatesA-1715
German Research Foundation (DFG)GermanySU 726/6-1

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description