4LWO

Crystal structure of PRMT6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Arginine Methyltransferase 6 from Trypanosoma brucei

Wang, C.Zhu, Y.Chen, J.Li, X.Peng, J.Chen, J.Zou, Y.Zhang, Z.Jin, H.Yang, P.Wu, J.Niu, L.Gong, Q.Teng, M.Shi, Y.

(2014) PLoS One 9: e87267-e87267

  • DOI: https://doi.org/10.1371/journal.pone.0087267
  • Primary Citation of Related Structures:  
    4LWO, 4LWP

  • PubMed Abstract: 

    Arginine methylation plays vital roles in the cellular functions of the protozoan Trypanosoma brucei. The T. brucei arginine methyltransferase 6 (TbPRMT6) is a type I arginine methyltransferase homologous to human PRMT6. In this study, we report the crystal structures of apo-TbPRMT6 and its complex with the reaction product S-adenosyl-homocysteine (SAH). The structure of apo-TbPRMT6 displays several features that are different from those of type I PRMTs that were structurally characterized previously, including four stretches of insertion, the absence of strand β15, and a distinct dimerization arm. The comparison of the apo-TbPRMT6 and SAH-TbPRMT6 structures revealed the fine rearrangements in the active site upon SAH binding. The isothermal titration calorimetry results demonstrated that SAH binding greatly increases the affinity of TbPRMT6 to a substrate peptide derived from bovine histone H4. The western blotting and mass spectrometry results revealed that TbPRMT6 methylates bovine histone H4 tail at arginine 3 but cannot methylate several T. brucei histone tails. In summary, our results highlight the structural differences between TbPRMT6 and other type I PRMTs and reveal that the active site rearrangement upon SAH binding is important for the substrate binding of TbPRMT6.


  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arginine N-methyltransferase, putativeA [auth B],
B [auth A],
C [auth E],
D [auth G]
368Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: Tb927.5.3960
UniProt
Find proteins for Q57U70 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q57U70 
Go to UniProtKB:  Q57U70
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57U70
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.903α = 90
b = 143.256β = 96.67
c = 75.603γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references